eaogorg.files.wordpress.com€¦ · Web view2020. 2. 11. · GEOCHEMISTRY ARTICLES – November 2019. Analytical Chemistry. Akinlua, A., Jochmann, M.A., Lorenzo-Parodi, N., Stojanovic,

GEOCHEMISTRY ARTICLES – November 2019

Analytical Chemistry

Akinlua, A., Jochmann, M.A., Lorenzo-Parodi, N., Stojanovic, N., Kaziur, W., Schmidt, T.C., 2019. A green approach for the extraction of diamondoids from petroleum source rock. Analytica Chimica Acta 1091, 23-29.

Andersen, S.I., 2019. Petroleum size exclusion chromatography: Mechanisms explaining the NMP front peak. Energy & Fuels 33, 10667-10677.

Borrego-Varillas, R., Nenov, A., Ganzer, L., Oriana, A., Manzoni, C., Tolomelli, A., Rivalta, I., Mukamel, S., Garavelli, M., Cerullo, G., 2019. Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules. Chemical Science 10, 9907-9921.

Bowden, S.A., Taylor, C.W., 2019. The application of surface enhanced Raman scattering to the detection of asphaltic petroleum in sediment extracts: deconvolving three component-mixtures using look-up tables of entire surface enhanced Raman spectra. Analytical Methods 11, 5846-5856.

Casado-Carmona, F.A., Alcudia-León, M.d.C., Lucena, R., Cárdenas, S., 2019. Portable stir membrane device for on-site environmental sampling and extraction. Journal of Chromatography A 1606, 360359.

Chen, Y., Xia, L., Liang, R., Lu, Z., Li, L., Huo, B., Li, G., Hu, Y., 2019. Advanced materials for sample preparation in recent decade. TrAC Trends in Analytical Chemistry 120, 115652.

Fujishima, K., Dziomba, S., Yano, H., Kebe, S.I., Guerrouache, M., Carbonnier, B., Rothschild, L.J., 2019. The non-destructive separation of diverse astrobiologically relevant organic molecules by customizable capillary zone electrophoresis and monolithic capillary electrochromatography. International Journal of Astrobiology 18, 562-574.

Psillakis, E., Koutela, N., Colussi, A.J., 2019. Vacuum-assisted headspace single-drop microextraction: Eliminating interfacial gas-phase limitations. Analytica Chimica Acta 1092, 9-16.

Wei, S., Liu, Y., Kou, X., Huang, S., Chen, G., Xu, L., Tong, Q., Zhu, F., Xu, J., Ouyang, G., 2019. Energy-efficient construction of thermally stable superhydrophobic nanoscale stacked lamellae based solid-phase microextraction coating for the determination of non-polar compounds. Analytica Chimica Acta 1092, 17-23.

Wichmann, C., Chhallani, M., Bocklitz, T., Rösch, P., Popp, J., 2019. Simulation of transportation and storage and their influence on Raman spectra of bacteria. Analytical Chemistry 91, 13688-13694.

GAS CHROMATOGRAPHY/GC×GC/GC-MS

García-Cicourel, A.R., van de Velde, B., Verduin, J., Janssen, H.-G., 2019. Comprehensive off-line silver phase liquid chromatography × gas chromatography with flame ionization and vacuum ultraviolet detection for the detailed characterization of mineral oil aromatic hydrocarbons. Journal of Chromatography A 1607, 460391.

Gröger, T.M., Käfer, U., Zimmermann, R., 2020. Gas chromatography in combination with fast high-resolution time-of-flight mass spectrometry: Technical overview and perspectives for data visualization. TrAC Trends in Analytical Chemistry 122, 115677.

Käfer, U., Gröger, T., Rohbogner, C.J., Struckmeier, D., Saraji-Bozorgzad, M.R., Wilharm, T., Zimmermann, R., 2019. Detailed chemical characterization of bunker fuels by high-resolution time-of-flight mass spectrometry hyphenated to GC × GC and thermal analysis. Energy & Fuels 33, 10745-10755.

Pojjanapornpun, S., Kulsing, C., Kakanopas, P., Nolvachai, Y., Aryusuk, K., Krisnangkura, K., Marriott, P.J., 2019. Simulation of peak position and response profiles in comprehensive two-dimensional gas chromatography. Journal of Chromatography A 1607, 460392.

Powers, J.B., Campagna, S.R., 2019. Design and evaluation of a gas chromatograph-atmospheric pressure chemical ionization interface for an Exactive Orbitrap mass spectrometer. Journal of The American Society for Mass Spectrometry 30, 2369-2379.

Prebihalo, S.E., Pinkerton, D.K., Synovec, R.E., 2019. Impact of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry experimental design on data trilinearity and parallel factor analysis deconvolution. Journal of Chromatography A 1605, 460368.

Rodríguez-Sánchez, S., Soria, A.C., Lebrón-Aguilar, R., Sanz, M.L., Ruiz-Matute, A.I., 2019. Evaluation of different ionic liquid stationary phases for the analysis of carbohydrates by gas chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry 411, 7461-7472.

Vyviurska, O., Špánik, I., 2020. Assessment of Tokaj varietal wines with comprehensive two-dimensional gas chromatography coupled to high resolution mass spectrometry. Microchemical Journal 152, 104385.

Wortberg, M., Kurz, J., 2019. Analytics 4.0: Online wastewater monitoring by GC and HPLC. Analytical and Bioanalytical Chemistry 411, 6783-6790.

IMAGING: AFM

Verlhac, B., Bachellier, N., Garnier, L., Ormaza, M., Abufager, P., Robles, R., Bocquet, M.L., Ternes, M., Lorente, N., Limot, L., 2019. Atomic-scale spin sensing with a single molecule at the apex of a scanning tunneling microscope. Science 366, 623-627.

IMAGING: SEM, TEM, HIM

Belilla, J., Moreira, D., Jardillier, L., Reboul, G., Benzerara, K., López-García, J.M., Bertolino, P., López-Archilla, A.I., López-García, P., 2019. Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area. Nature Ecology & Evolution 3, 1552-1561.

Benaiges-Fernandez, R., Palau, J., Offeddu, F.G., Cama, J., Urmeneta, J., Soler, J.M., Dold, B., 2019. Dissimilatory bioreduction of iron(III) oxides by Shewanella loihica under marine sediment conditions. Marine Environmental Research 151, 104782.

Cincotta, M.M., Perdrial, J.N., Shavitz, A., Libenson, A., Landsman-Gerjoi, M., Perdrial, N., Armfield, J., Adler, T., Shanley, J.B., 2019. Soil aggregates as a source of dissolved organic carbon to streams: An experimental study on the effect of solution chemistry on water extractable carbon. Frontiers in Environmental Science 7, 172. doi: 110.3389/fenvs.2019.00172.

Delarue, F., Robert, F., Derenne, S., Tartèse, R., Jauvion, C., Bernard, S., Pont, S., Gonzalez-Cano, A., Duhamel, R., Sugitani, K., 2020. Out of rock: A new look at the morphological and geochemical preservation of microfossils from the 3.46 Gyr-old Strelley Pool Formation. Precambrian Research 336, 105472.

Dong, T., Harris, N.B., 2020. The effect of thermal maturity on porosity development in the Upper Devonian –Lower Mississippian Woodford Shale, Permian Basin, US: Insights into the role of silica nanospheres and microcrystalline quartz on porosity preservation. International Journal of Coal Geology 217, 103346.

Guignard, G., 2019. Thirty-three years (1986–2019) of fossil plant cuticle studies using transmission electron microscopy: A review. Review of Palaeobotany and Palynology 271, 104097.

Hackley, P.C., Zhang, T., Jubb, A.M., Valentine, B.J., Dulong, F.T., Hatcherian, J.J., 2020. Organic petrography of Leonardian (Wolfcamp A) mudrocks and carbonates, Midland Basin, Texas: The fate of oil-prone sedimentary organic matter in the oil window. Marine and Petroleum Geology 112, 104086.

Ji, W., Hao, F., Schulz, H.-M., Song, Y., Tian, J., 2019. The architecture of organic matter and its pores in highly mature gas shales of the lower Silurian Longmaxi Formation in the upper Yangtze platform, south China. American Association of Petroleum Geologists Bulletin 103, 2909-2942.

Le Nagard, L., Zhu, X., Yuan, H., Benzerara, K., Bazylinski, D.A., Fradin, C., Besson, A., Swaraj, S., Stanescu, S., Belkhou, R., Hitchcock, A.P., 2019. Magnetite magnetosome biomineralization in Magnetospirillum magneticum strain AMB-1: A time course study. Chemical Geology 530, 119348.

Lévy, D., Aléon, J., Aléon-Toppani, A., Troadec, D., Duhamel, R., Gonzalez-Cano, A., Bureau, H., Khodja, H., 2019. NanoSIMS imaging of D/H ratios on FIB sections. Analytical Chemistry 91, 13763-13771.

Lindgren, P., Hallis, L., Hage, F.S., Lee, M.R., Parnell, J., Plan, A., Doye, A., MacLaren, I., 2019. A TEM and EELS study of carbon in a melt fragment from the Gardnos impact structure. Meteoritics & Planetary Science 54, 2698-2709.

Liu, D., Fan, Q., Papineau, D., Yu, N., Chu, Y., Wang, H., Qiu, X., Wang, X., 2020. Precipitation of protodolomite facilitated by sulfate-reducing bacteria: The role of capsule extracellular polymeric substances. Chemical Geology 533, 119415.

Liu, L., Ireland, T., Holden, P., Mavrogenes, J., 2020. The sign of Δ33S is independent of pyrite morphology. Chemical Geology 532, 119369.

Ma, Y., Ardakani, O.H., Zhong, N., Liu, H., Huang, H., Larter, S., Zhang, C., 2020. Possible pore structure deformation effects on the shale gas enrichment: An example from the Lower Cambrian shales of the Eastern Upper Yangtze Platform, South China. International Journal of Coal Geology 217, 103349.

Ma, Y., Zhong, N., Yao, L., Huang, H., Larter, S., Jiao, W., 2020. Shale gas desorption behavior and carbon isotopic variations of gases from canister desorption of two sets of gas shales in south China. Marine and Petroleum Geology 113, 104127.

Medunić, G., Grigore, M., Dai, S., Berti, D., Hochella, M.F., Mastalerz, M., Valentim, B., Guedes, A., Hower, J.C., 2020. Characterization of superhigh-organic-sulfur Raša coal, Istria, Croatia, and its environmental implication. International Journal of Coal Geology 217, 103344.

Mohanty, K.K., Tong, S., Miller, C., Zeng, T., Honarpour, M.M., Turek, E., Peck, D.D., 2019. Improved hydrocarbon recovery using mixtures of energizing chemicals in unconventional reservoirs. SPE-191644-PA 22, 1436-1448.

Motta, A., Berning, M., Boergens, K.M., Staffler, B., Beining, M., Loomba, S., Hennig, P., Wissler, H., Helmstaedter, M., 2019. Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science 366, eaay3134.

Oshima, M., Suzuki, K., Yoneda, J., Kato, A., Kida, M., Konno, Y., Muraoka, M., Jin, Y., Nagao, J., Tenma, N., 2019. Lithological properties of natural gas hydrate–bearing sediments in pressure-cores recovered from the Krishna–Godavari Basin. Marine and Petroleum Geology 108, 439-470.

Pang, Z., Tao, S., Zhang, Q., Zhang, T., Yang, J., Fan, J., Yuan, M., 2019. Enrichment factors and sweep spot evaluation of Jurassic tight oil in central Sichuan Basin, SW China. Petroleum Research 4, 334-347.

Pinheiro, F.L., Prado, G., Ito, S., Simon, J.D., Wakamatsu, K., Anelli, L.E., Andrade, J.A.F., Glass, K., 2019. Chemical characterization of pterosaur melanin challenges color inferences in extinct animals. Scientific Reports 9, 15947.

Rosenfeldt, S., Riese, C.N., Mickoleit, F., Schüler, D., Schenk, A.S., 2019. Probing the nanostructure and arrangement of bacterial magnetosomes by small-angle X-ray scattering. Applied and Environmental Microbiology 85, e01513-01519.

Saxena, N., Hows, A., Hofmann, R., Alpak, F.O., Dietderich, J., Appel, M., Freeman, J., De Jong, H., 2019. Rock properties from micro-CT images: Digital rock transforms for resolution, pore volume, and field of view. Advances in Water Resources 134, 103419.

Sun, M., Zhang, L., Hu, Q., Pan, Z., Yu, B., Sun, L., Bai, L., Fu, H., Zhang, Y., Zhang, C., Cheng, G., 2020. Multiscale connectivity characterization of marine shales in southern China by fluid intrusion, small-angle neutron scattering (SANS), and FIB-SEM. Marine and Petroleum Geology 112, 104101.

Sun, Z., Wang, Y., Wei, Z., Ni, Y., Wu, B., Li, J., Fan, W., Wang, G., Li, Y., 2019. Pore structure alteration characteristics of different mineralogical composition shale during shale-fracturing fluid physical-chemical interactions. Geofluids 2019, 5047643.

Takeshita, K., Yamada, T., Kawahara, Y., Narihiro, T., Ito, M., Kamagata, Y., Shinzato, N., 2019. Tripartite symbiosis of an anaerobic scuticociliate with two hydrogenosome-associated endosymbionts, a Holospora-related alphaproteobacterium and a methanogenic archaeon. Applied and Environmental Microbiology 85, e00854-00819.

Tang, G., Wang, G., An, Y., Zhang, H., 2019. Graphene oxide on microbially induced calcium carbonate precipitation. International Biodeterioration & Biodegradation 145, 104767.

Wacey, D., Eiloart, K., Saunders, M., 2019. Comparative multi-scale analysis of filamentous microfossils from the c. 850 Ma Bitter Springs Group and filaments from the c. 3460 Ma Apex chert. Journal of the Geological Society 176, 1247.

Wang, X., Liu, L., Wang, Y., Sheng, Y., Zheng, S., Luo, Z., 2019. Control of lithofacies on pore space of shale from Longmaxi Formation, southern Sichuan Basin. Acta Petrolei Sinica 40, 1192-1201

Yin, Z.-J., Lu, J., 2019. Virtual Palaeontology: when fossils illuminated by X-ray. Palaeoworld 28, 425-428.

Zhong, T., Liao, P., Chen, Q.-x., Li, N., Deng, H.-c., Liu, Q.-j., Luo, Y.-l., Lan, H.-x., Li, C.-y., 2019. Imaging the pore structure in geomaterials using rhodamine B covalently decorated magnetic nanoparticles. ACS Earth and Space Chemistry 3, 2482-2489.

IMAGING: XRAY CT

Akai, T., Alhammadi, A.M., Blunt, M.J., Bijeljic, B., 2019. Mechanisms of microscopic displacement during enhanced oil recovery in mixed-wet rocks revealed using direct numerical simulation. Transport in Porous Media 130, 731-749.

Alhosani, A., Scanziani, A., Lin, Q., Pan, Z., Bijeljic, B., Blunt, M.J., 2019. In situ pore-scale analysis of oil recovery during three-phase near-miscible CO2 injection in a water-wet carbonate rock. Advances in Water Resources 134, 103432.

Bensinger, J., Beckingham, L.E., 2020. CO2 storage in the Paluxy formation at the Kemper County CO2 storage complex: Pore network properties and simulated reactive permeability evolution. International Journal of Greenhouse Gas Control 93, 102887.

Broughton, P.L., 2020. Salt dissolution tectonism and microbial origin of drainage-line silcrete in the Lower Cretaceous Athabasca Oil Sands, foreland Alberta Basin. Marine and Petroleum Geology 112, 104099.

Gan, M., Zhang, L., Miao, X., Wang, Y., Fu, X., Bai, M., Li, X., 2019. Micro-CT characterization of wellbore cement degradation in SO4

2- bearing brine under geological CO2 storage environment. Geofluids 2019, 5164010.

Gupta, L.P., Tanikawa, W., Hamada, Y., Hirose, T., Ahagon, N., Sugihara, T., Abe, N., Nomura, S., Masaki, Y., Wu, H.Y., Lin, W., Kinoshita, M., Yamada, Y., 2019. Examination of gas hydrate-bearing deep ocean sediments by X-ray Computed Tomography and verification of physical property measurements of sediments. Marine and Petroleum Geology 108, 239-248.

Holland, M.E., Schultheiss, P.J., Roberts, J.A., 2019. Gas hydrate saturation and morphology from analysis of pressure cores acquired in the Bay of Bengal during expedition NGHP-02, offshore India. Marine and Petroleum Geology 108, 407-423.

Iglauer, S., Paluszny, A., Rahman, T., Zhang, Y., Wülling, W., Lebedev, M., 2019. Residual trapping of CO2 in an oil-filled, oil-wet sandstone core: Results of three-phase pore-scale imaging. Geophysical Research Letters 46, 11146-11154.


Niekus, M.J.L.T., Kozowyk, P.R.B., Langejans, G.H.J., Ngan-Tillard, D., van Keulen, H., van der Plicht, J., Cohen, K.M., van Wingerden, W., van Os, B., Smit, B.I., Amkreutz, L.W.S.W., Johansen, L., Verbaas, A., Dusseldorp, G.L., 2019. Middle Paleolithic complex technology and a Neandertal tar-backed tool from the Dutch North Sea. Proceedings of the National Academy of Sciences 116, 22081-22087.


Wang, D., Li, Y., Liu, C., Zhan, L., Lu, H., Li, C., Sun, J., Meng, Q., Liu, L., 2020. Study of hydrate occupancy, morphology and microstructure evolution with hydrate dissociation in sediment matrices using X-ray micro-CT. Marine and Petroleum Geology 113, 104138.

Zhang, K., Cheng, Y., Li, W., Hao, C., Hu, B., Jiang, J., 2019. Microcrystalline characterization and morphological structure of tectonic anthracite using XRD, liquid nitrogen adsorption, mercury porosimetry, and micro-CT. Energy & Fuels 33, 10844-10851.

Also see under Evolution/Paleontology/Palynology: Virtual Palaeontology: when fossils reconstructed by X-ray tomography. Paleoworld, 29(4), 425-576. Edited by Zong-Jun Yin, Jing Lu

LIQUID CHROMATOGRAPHY/LC-MS/SFC

Bäurer, S., Ferri, M., Carotti, A., Neubauer, S., Sardella, R., Lämmerhofer, M., 2020. Mixed-mode chromatography characteristics of chiralpak ZWIX(+) and ZWIX(−) and elucidation of their chromatographic orthogonality for LC × LC application. Analytica Chimica Acta 1093, 168-179.

Kot, D., Macko, T., Arndt, J.-H., Brüll, R., 2019. Porous graphite as platform for the separation and characterization of synthetic polymers – an overview. Journal of Chromatography A 1606, 360038.

Li, J., Wang, Q.-L., Liu, Y., Ke, Y., Fan, Q.-Q., Zhou, P., An, M.-C., Liu, H.-M., 2019. Simultaneous determination of 24 free amino acids in MGC803 cells by hydrophilic interaction liquid chromatography with tandem mass spectrometry. Journal of Chromatography B 1132, 121792.

Roy, D., Wahab, M.F., Berger, T.A., Armstrong, D.W., 2019. Ramifications and insights on the role of water in chiral sub/supercritical fluid chromatography. Analytical Chemistry 91, 14672-14680.

Stoll, D.R., Lhotka, H.R., Harmes, D.C., Madigan, B., Hsiao, J.J., Staples, G.O., 2019. High resolution two-dimensional liquid chromatography coupled with mass spectrometry for robust and sensitive characterization of therapeutic antibodies at the peptide level. Journal of Chromatography B 1134-1135, 121832.

Subirats, X., Abraham, M.H., Rosés, M., 2019. Characterization of hydrophilic interaction liquid chromatography retention by a linear free energy relationship. Comparison to reversed- and normal-phase retentions. Analytica Chimica Acta 1092, 132-143.


Zangrando, R., Zanella, V., Karroca, O., Barbaro, E., Kehrwald, N.M., Battistel, D., Morabito, E., Gambaro, A., Barbante, C., 2020. Dissolved organic matter in the deep TALDICE ice core: A nano-UPLC-nano-ESI-HRMS method. Science of The Total Environment 700, 134432.

MASS SPECTROSCOPY/ICR-FTMS/ORBITRAP

Benk, S.A., Yan, L., Lehmann, R., Roth, V.-N., Schwab, V.F., Totsche, K.U., Küsel, K., Gleixner, G., 2019. Fueling diversity in the subsurface: Composition and age of dissolved organic matter in the critical zone. Frontiers in Earth Science 7, 296. doi: 210.3389/feart.2019.00296.

Choi, J.H., Jang, E., Yoon, Y.J., Park, J.Y., Kim, T.W., Becagli, S., Caiazzo, L., Cappelletti, D., Krejci, R., Eleftheriadis, K., Park, K.T., Jang, K.S., 2019. Influence of biogenic organics on the chemical composition of Arctic aerosols. Global Biogeochemical Cycles 33, 1238-1250.

Choyke, S., Ferguson, P.L., 2019. Molecular characterization of nonionic surfactant components of the Corexit® 9500 oil spill dispersant by high-resolution mass spectrometry. Rapid Communications in Mass Spectrometry 33, 1683-1694.

Hansen, C.T., Niggemann, J., Giebel, H.-A., Simon, M., Bach, W., Dittmar, T., 2019. Biodegradability of hydrothermally altered deep-sea dissolved organic matter. Marine Chemistry 217, 103706.

Li, D., Yang, X., Zhou, Z., Jiang, B., Tawfik, A., Zhao, S., Meng, F., 2019. Molecular traits of phenolic moieties in dissolved organic matter: Linkages with membrane fouling development. Environment International 133, 105202.

Liu, S., He, Z., Tang, Z., Liu, L., Hou, J., Li, T., Zhang, Y., Shi, Q., Giesy, J.P., Wu, F., 2020. Linking the molecular composition of autochthonous dissolved organic matter to source identification for freshwater lake ecosystems by combination of optical spectroscopy and FT-ICR-MS analysis. Science of The Total Environment 703, 134764.

McDonough, L.K., O'Carroll, D.M., Meredith, K., Andersen, M.S., Brügger, C., Huang, H., Rutlidge, H., Behnke, M.I., Spencer, R.G.M., McKenna, A., Marjo, C.E., Oudone, P., Baker, A., 2020. Changes in groundwater dissolved organic matter character in a coastal sand aquifer due to rainfall recharge. Water Research 169, 115201.


Snyder, D.T., Panczyk, E., Stiving, A.Q., Gilbert, J.D., Somogyi, A., Kaplan, D., Wysocki, V., 2019. Design and performance of a second-generation surface-induced dissociation cell for Fourier transform ion cyclotron resonance mass spectrometry of native protein complexes. Analytical Chemistry 91, 14049-14057.

Solihat, N.N., Yustiawati, Kim, S., Kim, S., 2019. Elucidating molecular level impact of peat fire on soil organic matter by laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry. Analytical and Bioanalytical Chemistry 411, 7303-7313.

Textor, S.R., Wickland, K.P., Podgorski, D.C., Johnston, S.E., Spencer, R.G.M., 2019. Dissolved organic carbon turnover in permafrost-influenced watersheds of interior Alaska: Molecular insights and the priming effect. Frontiers in Earth Science 7, 275. doi: 210.3389/feart.2019.00275.

Wang, H., Cheng, Z., Sun, Z., Zhu, N., Yuan, H., Lou, Z., Chen, X., 2020. Molecular insight into variations of dissolved organic matters in leachates along China’s largest A/O-MBR-NF process to improve the removal efficiency. Chemosphere 243, 125354.

Zhu, G., Wang, P., Wang, M., Zhang, Z., Shi, Q., 2019. Occurrence and origins of thiols in deep strata crude oils, Tarim Basin, China. ACS Earth and Space Chemistry 3, 2499-2509.

MASS SPECTROSCOPY/OTHER

Aoyagi, S., Kodama, Y., Passarelli, M.K., Vorng, J.-L., Kawashima, T., Yoshikiyo, K., Yamamoto, T., Gilmore, I.S., 2019. OrbiSIMS imaging identifies molecular constituents of the perialgal vacuole membrane of Paramecium bursaria with symbiotic Chlorella variabilis. Analytical Chemistry 91, 14545-14551.

Bastrup, J., Birkelund, S., Asuni, A.A., Volbracht, C., Stensballe, A., 2019. Dual strategy for reduced signal-suppression effects in matrix-assisted laser desorption/ionization mass spectrometry imaging. Rapid Communications in Mass Spectrometry 33, 1711-1721.

Bian, J., Olesik, S.V., 2020. Polyvinylpyrrolidone composite nanofibers as efficient substrates for surface-assisted laser desorption/ionization mass spectrometry. International Journal of Mass Spectrometry 448, 116253.

Bowman, A.P., Heeren, R.M.A., Ellis, S.R., 2019. Advances in mass spectrometry imaging enabling observation of localised lipid biochemistry within tissues. TrAC Trends in Analytical Chemistry 120, 115197.

Cho, E., Riches, E., Palmer, M., Giles, K., Ujma, J., Kim, S., 2019. Isolation of crude oil peaks differing by m/z ∼0.1 via tandem mass spectrometry using a cyclic ion mobility-mass spectrometer. Analytical Chemistry 91, 14268-14274.


DeBlase, A.F., Bruening, C.R., Lewis, W.K., Bunker, C.E., 2019. In situ diagnostic of supercritical fuel surrogates: Probing heterogeneous catalysis by collision-induced dissociation in a molecular beam tandem mass spectrometer. Energy & Fuels 33, 10861-10867.

Ellis, B.M., Fischer, C.N., Martin, L.B., Bachmann, B.O., McLean, J.A., 2019. Spatiochemically profiling microbial interactions with membrane scaffolded desorption electrospray ionization-ion mobility-imaging mass spectrometry and unsupervised segmentation. Analytical Chemistry 91, 13703-13711.

Hale, O.J., Cramer, R., 2019. Atmospheric pressure ultraviolet laser desorption and ionization from liquid samples for native mass spectrometry. Analytical Chemistry 91, 14192-14197.

Kang, Y., Schneider, B.B., Bedford, L., Covey, T.R., 2019. Design characteristics to eliminate the need for parameter optimization in nanoflow ESI-MS. Journal of The American Society for Mass Spectrometry 30, 2347-2357.


Lowenthal, M.S., Quittman, E., Phinney, K.W., 2019. Absolute quantification of RNA or DNA using acid hydrolysis and mass spectrometry. Analytical Chemistry 91, 14569-14576.

Martens, J., van Outersterp, R.E., Vreeken, R.J., Cuyckens, F., Coene, K.L.M., Engelke, U.F., Kluijtmans, L.A.J., Wevers, R.A., Buydens, L.M.C., Redlich, B., Berden, G., Oomens, J., 2020. Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective. Analytica Chimica Acta 1093, 1-15.

Peter, K.T., Wu, C., Tian, Z., Kolodziej, E.P., 2019. Application of nontarget high resolution mass spectrometry data to quantitative source apportionment. Environmental Science & Technology 53, 12257-12268.

Snyder, D.T., Szalwinski, L.J., St. John, Z., Cooks, R.G., 2019. Two-dimensional tandem mass spectrometry in a single scan on a linear quadrupole ion trap. Analytical Chemistry 91, 13752-13762.

Spraggins, J.M., Djambazova, K.V., Rivera, E.S., Migas, L.G., Neumann, E.K., Fuetterer, A., Suetering, J., Goedecke, N., Ly, A., Van de Plas, R., Caprioli, R.M., 2019. High-performance molecular imaging with MALDI trapped ion-mobility time-of-flight (timsTOF) mass spectrometry. Analytical Chemistry 91, 14552-14560.

METABOLOMICS/LIPIDOMICS

Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., Mashaghi, A., Hankemeier, T., 2019. Single-cell metabolomics by mass spectrometry: advances, challenges, and future applications. TrAC Trends in Analytical Chemistry 120, 115436.

Bachmann, R., Jilani, A., Ibrahim, H., Bahmann, D., Lang, C., Fischer, M., Bisping, B., Hackl, T., 2019. Signal pattern plot: a simple tool for time-dependent metabolomics studies by 1H NMR spectroscopy. Analytical and Bioanalytical Chemistry 411, 6857-6866.

Balcells, C., Foguet, C., Tarragó-Celada, J., de Atauri, P., Marin, S., Cascante, M., 2019. Tracing metabolic fluxes using mass spectrometry: Stable isotope-resolved metabolomics in health and disease. TrAC Trends in Analytical Chemistry 120, 115371.

Bonner, R., Hopfgartner, G., 2019. SWATH data independent acquisition mass spectrometry for metabolomics. TrAC Trends in Analytical Chemistry 120, 115278.


Chang, Q., Peng, Y.e., Shi, B., Hu, S., Shuai, Q., 2019. Rapid screening of new organic sulfates and alkaloids in single plant cells using nanospray high-resolution mass spectrometry. Analytical Methods 11, 5359-5365.

Cooper, B.T., Yan, X., Simón-Manso, Y., Tchekhovskoi, D.V., Mirokhin, Y.A., Stein, S.E., 2019. Hybrid search: A method for identifying metabolites absent from tandem mass spectrometry libraries. Analytical Chemistry 91, 13924-13932.

Ellis, B.M., Fischer, C.N., Martin, L.B., Bachmann, B.O., McLean, J.A., 2019. Spatiochemically profiling microbial interactions with membrane scaffolded desorption

electrospray ionization-ion mobility-imaging mass spectrometry and unsupervised segmentation. Analytical Chemistry 91, 13703-13711.

Griffiths, W.J., Wang, Y., 2019. Sterolomics in biology, biochemistry, medicine. TrAC Trends in Analytical Chemistry 120, 115280.

Hu, C., Wang, C., He, L., Han, X., 2019. Novel strategies for enhancing shotgun lipidomics for comprehensive analysis of cellular lipidomes. TrAC Trends in Analytical Chemistry 120, 115330.

Hu, Y., Cai, B., Huan, T., 2019. Enhancing metabolome coverage in data-dependent LC–MS/MS analysis through an integrated feature extraction strategy. Analytical Chemistry 91, 14433-14441.

Li, L., Zhong, S., Shen, X., Li, Q., Xu, W., Tao, Y., Yin, H., 2019. Recent development on liquid chromatography-mass spectrometry analysis of oxidized lipids. Free Radical Biology and Medicine 144, 16-34.

Liang, D., Li, M., Wei, R., Wang, J., Li, Y., Jia, W., Chen, T., 2019. Strategy for intercorrelation identification between metabolome and microbiome. Analytical Chemistry 91, 14424-14432.

Lv, W., Shi, X., Wang, S., Xu, G., 2019. Multidimensional liquid chromatography-mass spectrometry for metabolomic and lipidomic analyses. TrAC Trends in Analytical Chemistry 120, 115302.


Miggiels, P., Wouters, B., van Westen, G.J.P., Dubbelman, A.-C., Hankemeier, T., 2019. Novel technologies for metabolomics: More for less. TrAC Trends in Analytical Chemistry 120, 115323.

Nash, W.J., Dunn, W.B., 2019. From mass to metabolite in human untargeted metabolomics: Recent advances in annotation of metabolites applying liquid chromatography-mass spectrometry data. TrAC Trends in Analytical Chemistry 120, 115324.

Ni, Z., Goracci, L., Cruciani, G., Fedorova, M., 2019. Computational solutions in redox lipidomics – Current strategies and future perspectives. Free Radical Biology and Medicine 144, 110-123.

Řezanka, T., Vítová, M., Lukavský, J., Nedbalová, L., Kolouchová, I., 2019. Rapid screening of very long-chain fatty acids from microorganisms. Journal of Chromatography A 1605, 460365.

Shi, X., Wang, S., Jasbi, P., Turner, C., Hrovat, J., Wei, Y., Liu, J., Gu, H., 2019. Database-assisted globally optimized targeted mass spectrometry (dGOT-MS): Broad and reliable metabolomics analysis with enhanced identification. Analytical Chemistry 91.

Takis, P.G., Ghini, V., Tenori, L., Turano, P., Luchinat, C., 2019. Uniqueness of the NMR approach to metabolomics. TrAC Trends in Analytical Chemistry 120, 115300.

Thompson, J.W., Adams, K.J., Adamski, J., Asad, Y., Borts, D., Bowden, J.A., Byram, G., Dang, V., Dunn, W.B., Fernandez, F., Fiehn, O., Gaul, D.A., Hühmer, A.F.R., Kalli, A., Koal, T., Koeniger, S., Mandal, R., Meier, F., Naser, F.J., O’Neil, D., Pal, A., Patti, G.J., Pham-Tuan, H., Prehn, C., Raynaud, F.I., Shen, T., Southam, A.D., St. John-Williams, L., Sulek, K., Vasilopoulou, C.G., Viant, M., Winder, C.L., Wishart, D., Zhang, L., Zheng, J., Moseley, M.A., 2019. International ring trial of a high resolution targeted metabolomics and lipidomics platform for serum and plasma analysis. Analytical Chemistry 91, 14407-14416.

Wang, J., Han, X., 2019. Analytical challenges of shotgun lipidomics at different resolution of measurements. TrAC Trends in Analytical Chemistry 121, 115697.

Zaitsu, K., Noda, S., Ohara, T., Murata, T., Funatsu, S., Ogata, K., Ishii, A., Iguchi, A., 2019. Optimal inter-batch normalization method for GC/MS/MS-based targeted metabolomics with special attention to centrifugal concentration. Analytical and Bioanalytical Chemistry 411, 6983-6994.

PUPPYOMICS

Griscti, O., Camilleri, L., 2020. The impact of dog therapy on nursing students’ heart rates and ability to pay attention in class. International Journal of Educational Research 99, 101498.

Overall, K.L., Dunham, A.E., Scheifele, P., Sonstrom Malowski, K., 2019. Fear of noises affects canine problem solving behavior and locomotion in standardized cognitive tests. Applied Animal Behaviour Science 221, 104863.

Archaeological/Art Organic Chemistry

Antonio, M.L., Gao, Z., Moots, H.M., Lucci, M., Candilio, F., Sawyer, S., Oberreiter, V., Calderon, D., Devitofranceschi, K., Aikens, R.C., Aneli, S., Bartoli, F., Bedini, A., Cheronet, O., Cotter, D.J., Fernandes, D.M., Gasperetti, G., Grifoni, R., Guidi, A., La Pastina, F., Loreti, E., Manacorda, D., Matullo, G., Morretta, S., Nava, A., Fiocchi Nicolai, V., Nomi, F., Pavolini, C., Pentiricci, M., Pergola, P., Piranomonte, M., Schmidt, R., Spinola, G., Sperduti, A., Rubini, M., Bondioli, L., Coppa, A., Pinhasi, R., Pritchard, J.K., 2019. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science 366, 708-714.

Dickson, J.H., Oeggl, K.D., Kofler, W., Hofbauer, W.K., Porley, R., Rothero, G.P., Schmidl, A., Heiss, A.G., 2019. Seventy-five mosses and liverworts found frozen with the late Neolithic Tyrolean Iceman: Origins, taphonomy and the Iceman’s last journey. PLOS ONE 14, e0223752.

Hardy, K., 2019. Paleomedicine and the use of plant secondary compounds in the Paleolithic and Early Neolithic. Evolutionary Anthropology: Issues, News, and Reviews 28, 60-71.

Jones, R.K., Piper, P.J., Wood, R., Nguyen, A.T., Oxenham, M.F., 2019. The Neolithic transition in Vietnam: Assessing evidence for early pig management and domesticated dog. Journal of Archaeological Science: Reports 28, 102042.

Kaal, J., Martín Seijo, M., Oliveira, C., Wagner-Wysiecka, E., McCoy, V.E., Solórzano Kraemer, M.M., Kerner, A., Wenig, P., Mayo, C., Mayo, J., 2020. Golden artefacts, resin figurines, body adhesives and tomb sediments from the pre-Columbian burial site El Caño (Gran Coclé, Panamá): Tracing organic contents using molecular archaeometry. Journal of Archaeological Science 113, 105045.

Kerudin, A., Müller, R., Buckberry, J., Knüsel, C.J., Brown, T.A., 2019. Ancient Mycobacterium leprae genomes from the mediaeval sites of Chichester and Raunds in England. Journal of Archaeological Science 112, 105035.

La Nasa, J., Modugno, F., Colombini, M.P., Degano, I., 2019. Validation study of selected ion flow tube-mass spectrometry (SIFT-MS) in heritage science: Characterization of natural and synthetic paint varnishes by portable mass spectrometry. Journal of The American Society for Mass Spectrometry 30, 2250-2258.

Luong, S., Tocheri, M.W., Hayes, E., Sutikna, T., Fullagar, R., Saptomo, E.W., Jatmiko, Roberts, R.G., 2019. Combined organic biomarker and use-wear analyses of stone artefacts from Liang Bua, Flores, Indonesia. Scientific Reports 9, 17553.

MacDonald, B.L., Stalla, D., He, X., Rahemtulla, F., Emerson, D., Dube, P.A., Maschmann, M.R., Klesner, C.E., White, T.A., 2019. Hunter-gatherers harvested and heated microbial biogenic iron oxides to produce rock art pigment. Scientific Reports 9, 17070.

Mittnik, A., Massy, K., Knipper, C., Wittenborn, F., Friedrich, R., Pfrengle, S., Burri, M., Carlichi-Witjes, N., Deeg, H., Furtwängler, A., Harbeck, M., von Heyking, K., Kociumaka, C., Kucukkalipci, I., Lindauer, S., Metz, S., Staskiewicz, A., Thiel, A., Wahl, J., Haak, W., Pernicka, E., Schiffels, S., Stockhammer, P.W., Krause, J., 2019. Kinship-based social inequality in Bronze Age Europe. Science 366, 731-734.

Negi, A., Sarethy, I.P., 2019. Microbial biodeterioration of cultural heritage: Events, colonization, and analyses. Microbial Ecology 78, 1014-1029.


Perini, N., Mercuri, F., Thaller, M.C., Orlanducci, S., Castiello, D., Talarico, V., Migliore, L., 2019. The stain of the original salt: Red heats on chrome tanned leathers and purple spots on ancient parchments are two sides of the same ecological coin. Frontiers in Microbiology 10, 2459. doi: 2410.3389/fmicb.2019.02459.

Rodríguez-Hidalgo, A., Morales, J.I., Cebrià, A., Courtenay, L.A., Fernández-Marchena, J.L., García-Argudo, G., Marín, J., Saladié, P., Soto, M., Tejero, J.M., Fullola, J.M., 2019. The Châtelperronian Neanderthals of Cova Foradada (Calafell, Spain) used imperial eagle phalanges for symbolic purposes. Science Advances 5, eaax1984.

Sánchez, A., Tuñón, J.A., Parras, D.J., Montejo, M., Lechuga, M.A., Ceprián, B., Soto, M., Luque, Á., 2019. MRS, EDXRF and GC–MS analysis for research on the ritual and funerary areas of Cerro de los Vientos (Baeza, Jaén, Spain). Native and Eastern Mediterranean influences. Journal of Archaeological Science: Reports 28, 102026.

Wade, L., 2019. Immigrants from the Middle East shaped Rome. Science 366, 673.

Zilhão, J., 2019. Tar adhesives, Neandertals, and the tyranny of the discontinuous mind. Proceedings of the National Academy of Sciences 116, 21966-21968.

Biochemistry

Creighbaum, A.J., Ticak, T., Shinde, S., Wang, X., Ferguson, D.J., 2019. Examination of the glycine betaine-dependent methylotrophic methanogenesis pathway: Insights into anaerobic quaternary amine methylotrophy. Frontiers in Microbiology 10, 2572. doi: 2510.3389/fmicb.2019.02572.

Farley, K.R., Metcalf, W.W., 2019. The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea. FEMS Microbiology Letters 366.

Fenibo, O.E., Ijoma, N.G., Selvarajan, R., Chikere, B.C., 2019. Microbial surfactants: The next generation multifunctional biomolecules for applications in the petroleum industry and its associated environmental remediation. Microorganisms 7, 10.3390/microorganisms7110581.

Hanson, J.R., Nichols, T., Mukhrish, Y., Bagley, M.C., 2019. Diterpenoids of terrestrial origin. Natural Product Reports 36, 1499-1512.

Ishibashi, Y., Aoki, K., Okino, N., Hayashi, M., Ito, M., 2019. A thraustochytrid-specific lipase/phospholipase with unique positional specificity contributes to microbial competition and fatty acid acquisition from the environment. Scientific Reports 9, 16357.

Kallscheuer, N., Moreira, C., Airs, R., Llewellyn, C.A., Wiegand, S., Jogler, C., Lage, O.M., 2019. Pink- and orange-pigmented Planctomycetes produce saproxanthin-type carotenoids including a rare C45 carotenoid. Environmental Microbiology Reports 11, 741-748.

Müller, V., 2019. New horizons in acetogenic conversion of one-carbon substrates and biological hydrogen storage. Trends in Biotechnology 37, 1344-1354.

Pearson, A., 2019. Resolving a piece of the archaeal lipid puzzle. Proceedings of the National Academy of Sciences 116, 22423-22425.


Schada von Borzyskowski, L., Severi, F., Krüger, K., Hermann, L., Gilardet, A., Sippel, F., Pommerenke, B., Claus, P., Cortina, N.S., Glatter, T., Zauner, S., Zarzycki, J., Fuchs, B.M., Bremer, E., Maier, U.G., Amann, R.I., Erb, T.J., 2019. Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle. Nature 575, 500-504.

Senik, S.V., Psurtseva, N.V., Shavarda, A.L., Kotlova, E.R., 2019. Role of lipids in the thermal plasticity of basidial fungus Favolaschia manipularis. Canadian Journal of Microbiology 65, 870-879.

van Santen, J.A., Jacob, G., Singh, A.L., Aniebok, V., Balunas, M.J., Bunsko, D., Neto, F.C., Castaño-Espriu, L., Chang, C., Clark, T.N., Cleary Little, J.L., Delgadillo, D.A., Dorrestein, P.C., Duncan, K.R., Egan, J.M., Galey, M.M., Haeckl, F.P.J., Hua, A., Hughes, A.H., Iskakova, D., Khadilkar, A., Lee, J.-H., Lee, S., LeGrow, N., Liu, D.Y., Macho, J.M., McCaughey, C.S., Medema, M.H., Neupane, R.P., O’Donnell, T.J., Paula, J.S., Sanchez, L.M., Shaikh, A.F., Soldatou, S., Terlouw, B.R., Tran, T.A., Valentine, M., van der Hooft, J.J.J., Vo, D.A., Wang, M., Wilson, D., Zink, K.E., Linington, R.G., 2019. The Natural Products Atlas: An open access knowledge base for microbial natural products discovery. ACS Central Science 5, 1824-1833.

Vaníčková, L., Pompeiano, A., Maděra, P., Massad, T.J., Vahalík, P., 2020. Terpenoid profiles of resin in the genus Dracaena are species specific. Phytochemistry 170, 112197.

Zeng, Z., Liu, X.-L., Farley, K.R., Wei, J.H., Metcalf, W.W., Summons, R.E., Welander, P.V., 2019. GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean. Proceedings of the National Academy of Sciences 116, 22505-22511.

Biodegradation

Bidja Abena, M.T., Sodbaatar, N., Li, T., Damdinsuren, N., Choidash, B., Zhong, W., 2019. Crude oil biodegradation by newly isolated bacterial strains and their consortium under soil microcosm experiment. Applied Biochemistry and Biotechnology 189, 1223-1244.

Cazarolli, J.C., Silva, T.L., da Camara Ribas, R.K., da Fontoura Xavier Costa, L., de Moura, T., Galeazzi, C.F., Dallé da Rosa, P., Kenne, D.C., Carvalho, Â.R., Valente, P., Pizzolato, T.M., Correa, C., Ferrão, M.F., Guedes Frazzon, A.P., Bento, F.M., 2020. Deterioration potential of Aureobasidium pullulans on biodiesel, diesel, and B20 blend. International Biodeterioration & Biodegradation 147, 104839.

Ebrahimi, A., Schwartzman, J., Cordero, O.X., 2019. Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria. Proceedings of the National Academy of Sciences 116, 23309-23316.

Gong, D., Zhang, Y., Guo, W., Qi, R., Lu, S., Wu, W, 2019. Identification of secondary microbial methane and biodegradation: Case study from Luliang oil and gas field, Junggar Basin, China. Journal of Natural Gas Geoscience 4, 267-278.


He, S., Ni, Y., Lu, L., Chai, Q., Liu, H., Yang, C., 2019. Enhanced biodegradation of n-hexane by Pseudomonas sp. strain NEE2. Scientific Reports 9, 16615.

He, S., Ni, Y., Lu, L., Chai, Q., Yu, T., Shen, Z., Yang, C., 2020. Simultaneous degradation of n-hexane and production of biosurfactants by Pseudomonas sp. strain NEE2 isolated from oil-contaminated soils. Chemosphere 242, 125237.

Huang, H., Yu, H., Qi, M., Liu, Z., Wang, H., Lu, Z., 2019. Enrichment and characterization of a highly efficient tetrahydrofuran-degrading bacterial culture. Biodegradation 30, 467-479.


Smułek, W., Sydow, M., Zabielska-Matejuk, J., Kaczorek, E., 2020. Bacteria involved in biodegradation of creosote PAH – A case study of long-term contaminated industrial area. Ecotoxicology and Environmental Safety 187, 109843.

Vergeynst, L., Greer, C.W., Mosbech, A., Gustavson, K., Meire, L., Poulsen, K.G., Christensen, J.H., 2019. Biodegradation, photo-oxidation, and dissolution of petroleum compounds in an Arctic fjord during summer. Environmental Science & Technology 53, 12197-12206.

Wu, K., Lu, K., Dai, M., Liu, Z., 2019. The bioavailability of riverine dissolved organic matter in coastal marine waters of southern Texas. Estuarine, Coastal and Shelf Science 231, 106477.

BIODEGRADATION PATHWAYS/GENOMICS

Gibu, N., Kasai, D., Ikawa, T., Akiyama, E., Fukuda, M., 2019. Characterization and transcriptional regulation of n-alkane hydroxylase gene cluster of Rhodococcus jostii RHA1. Microorganisms 7, 10.3390/microorganisms7110479.

Mislan, M., Gates, I.D., 2019. Release of sugars and fatty acids from heavy oil biodegradation by common hydrolytic enzymes. Scientific Reports 9, 15584.

Muccee, F., Ejaz, S., Riaz, N., 2019. Toluene degradation via a unique metabolic route in indigenous bacterial species. Archives of Microbiology 201, 1369-1383.

Panigrahy, N., Barik, M., Sahoo, R.K., Sahoo, N.K., 2020. Metabolic profile analysis and kinetics of p-cresol biodegradation by an indigenous Pseudomonas citronellolis NS1 isolated from coke oven wastewater. International Biodeterioration & Biodegradation 147, 104837.

Shi, K., Xue, J., Xiao, X., Qiao, Y., Wu, Y., Gao, Y., 2019. Mechanism of degrading petroleum hydrocarbons by compound marine petroleum-degrading bacteria: Surface adsorption, cell uptake, and biodegradation. Energy & Fuels 33, 11373-11379.

Sieber, C.M.K., Paul, B.G., Castelle, C.J., Hu, P., Tringe, S.G., Valentine, D.L., Andersen, G.L., Banfield, J.F., 2019. Unusual metabolism and hypervariation in the genome of a Gracilibacterium (BD1-5) from an oil-degrading community. mBio 10, e02128-02119.

Biofuels/Biomass/Bioengineering

Anto, S., Mukherjee, S.S., Muthappa, R., Mathimani, T., Deviram, G., Kumar, S.S., Verma, T.N., Pugazhendhi, A., 2020. Algae as green energy reserve: Technological outlook on biofuel production. Chemosphere 242, 125079.

Athanasakoglou, A., Kampranis, S.C., 2019. Diatom isoprenoids: Advances and biotechnological potential. Biotechnology Advances 37, 107417.

Bastidas-Oyanedel, J.-R., Schmidt, J.E. (eds.), 2019. Biorefinery. Integrated Sustainable Processes for Biomass Conversion to Biomaterials, Biofuels, and Fertilizers, Springer, 763 pp.

Chen, H., Luo, J., Liu, S., Yuan, Z., Guo, J., 2019. Microbial methane conversion to short-chain fatty acids using various electron acceptors in membrane biofilm reactors. Environmental Science & Technology 53, 12914-12922.

Chua, Y.W., Wu, H., Yu, Y., 2019. Interactions between low- and high-molecular-weight portions of lignin during fast pyrolysis at low temperatures. Energy & Fuels 33, 11173-11180.

Gilmour, D.J., 2019. Microalgae for biofuel production. Advances in Applied Microbiology 109, 1-30.

Rathinam, N.K., Gorky, Bibra, M., Salem, D.R., Sani, R.K., 2020. Bioelectrochemical approach for enhancing lignocellulose degradation and biofilm formation in Geobacillus strain WSUCF1. Bioresource Technology 295, 122271.

Stevens, J.C., Shi, J., 2019. Biocatalysis in ionic liquids for lignin valorization: Opportunities and recent developments. Biotechnology Advances 37, 107418.

Toor, M., Kumar, S.S., Malyan, S.K., Bishnoi, N.R., Mathimani, T., Rajendran, K., Pugazhendhi, A., 2020. An overview on bioethanol production from lignocellulosic feedstocks. Chemosphere 242, 125080.

Vlaskin, M.S., Grigorenko, A.V., Kotelev, M.S., Kopitsyn, D.S., Mazurova, K.M., Ivanov, E.V., 2019. Composition and properties of microalgae biomass hydrothermal liquefaction products. Chemistry and Technology of Fuels and Oils 55, 373-377.

Wang, Y., Liu, Y., He, J., Zhang, Y., 2019. Redox-neutral photocatalytic strategy for selective C–C bond cleavage of lignin and lignin models via PCET process. Science Bulletin 64, 1658-1666.

Wichmann, J., Lauersen, K.J., Kruse, O., 2020. Green algal hydrocarbon metabolism is an exceptional source of sustainable chemicals. Current Opinion in Biotechnology 61, 28-37.

Wu, S., Zhou, Y., Gerngross, D., Jeschek, M., Ward, T.R., 2019. Chemo-enzymatic cascades to produce cycloalkenes from bio-based resources. Nature Communications 10, 5060.

Yang, C., Wang, S., Ren, M., Li, Y., Song, W., 2019. Hydrothermal liquefaction of an animal carcass for biocrude oil. Energy & Fuels 33, 11302-11309.

Zhu, X., Chen, L., Chen, Y., Cao, Q., Liu, X., Li, D., 2019. Differences of methanogenesis between mesophilic and thermophilic in situ biogas-upgrading systems by hydrogen addition. Journal of Industrial Microbiology & Biotechnology 46, 1569-1581.

Biogeochemistry

Avetisyan, K., Eckert, W., Findlay, A.J., Kamyshny, A., 2019. Diurnal variations in sulfur transformations at the chemocline of a stratified freshwater lake. Biogeochemistry 146, 83-100.

Bergk Pinto, B., Maccario, L., Dommergue, A., Vogel, T.M., Larose, C., 2019. Do organic substrates drive microbial community interactions in Arctic snow? Frontiers in Microbiology 10, 2492. doi: 2410.3389/fmicb.2019.02492.

Bowles, M.W., Samarkin, V.A., Hunter, K.S., Finke, N., Teske, A.P., Girguis, P.R., Joye, S.B., 2019. Remarkable capacity for anaerobic oxidation of methane at high methane concentration. Geophysical Research Letters 46, 12192-12201.


Harfmann, J.L., Guillemette, F., Kaiser, K., Spencer, R.G.M., Chuang, C.-Y., Hernes, P.J., 2019. Convergence of terrestrial dissolved organic matter composition and the role of microbial buffering in aquatic ecosystems. Journal of Geophysical Research: Biogeosciences 124, 3125-3142.

Kelley, C.A., Bebout, B.M., Chanton, J.P., Detweiler, A.M., Frisbee, A., Nicholson, B.E., Poole, J., Tazaz, A., Winkler, C., 2019. The effect of bacterial sulfate reduction inhibition on the production and stable isotopic composition of methane in hypersaline environments. Aquatic Geochemistry 25, 237-251.

Palacios, P.A., Snoeyenbos-West, O., Löscher, C.R., Thamdrup, B., Rotaru, A.-E., 2019. Baltic Sea methanogens compete with acetogens for electrons from metallic iron. The ISME Journal 13, 3011-3023.

Pelikan, C., Jaussi, M., Wasmund, K., Seidenkrantz, M.-S., Pearce, C., Kuzyk, Z.Z.A., Herbold, C.W., Røy, H., Kjeldsen, K.U., Loy, A., 2019. Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments. Frontiers in Microbiology 10, 2558. doi: 2510.3389/fmicb.2019.02558.

Picard, A., Gartman, A., Cosmidis, J., Obst, M., Vidoudez, C., Clarke, D.R., Girguis, P.R., 2019. Authigenic metastable iron sulfide minerals preserve microbial organic carbon in anoxic environments. Chemical Geology 530, 119343.

Sharma, S., Steuer, R., 2019. Modelling microbial communities using biochemical resource allocation analysis. Journal of The Royal Society Interface 16, 20190474.

Tang, X., Yu, P., Tang, L., Zhou, M., Fan, C., Lu, Y., Mathieu, J., Xiong, W., Alvarez, P.J., 2019. Bacteriophages from arsenic-resistant bacteria-transduced resistance genes, which

changed arsenic speciation and increased soil toxicity. Environmental Science & Technology Letters 6, 675-680.

Uribe-Lorío, L., Brenes-Guillén, L., Hernández-Ascencio, W., Mora-Amador, R., González, G., Ramírez-Umaña, C.J., Díez, B., Pedrós-Alió, C., 2019. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. MicrobiologyOpen 8, e893.

Vonk, J.E., Tank, S.E., Walvoord, M.A., 2019. Integrating hydrology and biogeochemistry across frozen landscapes. Nature Communications 10, 5377.

Wilson, J., Ucharm, G., Beman, J.M., 2019. Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem. Scientific Reports 9, 16114.

BIOFILM/MICROBIAL INDUCED CORROSION

Cheng, Y., Hubbard, C.G., Geller, J.T., Chou, C., Voltolini, M., Engelbrektson, A.L., Coates, J.D., Ajo-Franklin, J.B., Wu, Y., 2019. Biofilm feedbacks alter hydrological characteristics of fractured rock impacting sulfidogenesis and treatment. Energy & Fuels 33, 10476-10486.

Jiang, Z., Shi, M., Shi, L., 2020. Degradation of organic contaminants and steel corrosion by the dissimilatory metal-reducing microorganisms Shewanella and Geobacter spp. International Biodeterioration & Biodegradation 147, 104842.

Sivadon, P., Barnier, C., Urios, L., Grimaud, R., 2019. Biofilm formation as a microbial strategy to assimilate particulate substrates. Environmental Microbiology Reports 11, 749-764.

Khan, S., Fu, P., 2020. Biotechnological perspectives on algae: a viable option for next generation biofuels. Current Opinion in Biotechnology 62, 146-152.

MICROBIAL MEDIATION OF MINERAL FORMATION/DEGRADATION



Eswayah, A.S., Hondow, N., Scheinost, A.C., Merroun, M., Romero-González, M., Smith, T.J., Gardiner, P.H.E., 2019. Methyl selenol as a precursor in selenite reduction to Se/S species by methane-oxidizing bacteria. Applied and Environmental Microbiology 85, e01379-01319.

Le Nagard, L., Zhu, X., Yuan, H., Benzerara, K., Bazylinski, D.A., Fradin, C., Besson, A., Swaraj, S., Stanescu, S., Belkhou, R., Hitchcock, A.P., 2019. Magnetite magnetosome

biomineralization in Magnetospirillum magneticum strain AMB-1: A time course study. Chemical Geology 530, 119348.



Carbon Cycle

Amesbury, M.J., Gallego-Sala, A., Loisel, J., 2019. Peatlands as prolific carbon sinks. Nature Geoscience 12, 880-881.

Basu, S., Verchovsky, A.B., Bogush, A., Jones, A.P., Jourdan, A.-L., 2019. Stability of organic carbon components in shale: Implications for carbon cycle. Frontiers in Earth Science 7, 297. doi: 210.3389/feart.2019.00297.

Bonan, G.B., Lombardozzi, D.L., Wieder, W.R., Oleson, K.W., Lawrence, D.M., Hoffman, F.M., Collier, N., 2019. Model structure and climate data uncertainty in historical simulations of the terrestrial carbon cycle (1850–2014). Global Biogeochemical Cycles 33, 1310-1326.

Horgby, Å., Segatto, P.L., Bertuzzo, E., Lauerwald, R., Lehner, B., Ulseth, A.J., Vennemann, T.W., Battin, T.J., 2019. Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains. Nature Communications 10, 4888.

Liu, Y., Chen, C., He, D., Chen, W., 2019. Deep carbon cycle in subduction zones. Science China Earth Sciences 62, 1764-1782.

Nichols, J.E., Peteet, D.M., 2019. Rapid expansion of northern peatlands and doubled estimate of carbon storage. Nature Geoscience 12, 917-921.

Silva, R.L., Duarte, L.V., Wach, G.D., Morrison, N., Campbell, T., 2020. Oceanic organic carbon as a possible first-order control on the carbon cycle during the Bathonian–Callovian. Global and Planetary Change 184, 103058.

Soudzilovskaia, N.A., van Bodegom, P.M., Terrer, C., Zelfde, M.v.t., McCallum, I., Luke McCormack, M., Fisher, J.B., Brundrett, M.C., de Sá, N.C., Tedersoo, L., 2019. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nature Communications 10, 5077.

Yue, P., Cui, X., Wu, W., Gong, Y., Li, K., Goulding, K., Liu, X., 2019. Impacts of precipitation, warming and nitrogen deposition on methane uptake in a temperate desert. Biogeochemistry 146, 17-29.

Zhao, J.-F., Peng, S.-S., Chen, M.-P., Wang, G.-Z., Cui, Y.-B., Liao, L.-G., Feng, J.-G., Zhu, B., Liu, W.-J., Yang, L.-Y., Tan, Z.-H., 2019. Tropical forest soils serve as substantial and persistent methane sinks. Scientific Reports 9, 16799.

Climate Change

Lüning, S., Schulte, L., Garcés-Pastor, S., Danladi, I.B., Gałka, M., 2019. The Medieval Climate Anomaly in the Mediterranean region. Paleoceanography and Paleoclimatology 34, 1625-1649.

Smith, T.P., Thomas, T.J.H., García-Carreras, B., Sal, S., Yvon-Durocher, G., Bell, T., Pawar, S., 2019. Community-level respiration of prokaryotic microbes may rise with global warming. Nature Communications 10, 5124.

Sun, J.-J., Li, H.-C., Wang, J., Zhao, H.-Y., Wang, S.-Z., Li, H.-K., Yang, Q.-N., Chou, C.-Y., Kashyap, S., 2019. Study of Jinchuan Mire in NE China II: Peatland development, carbon accumulation and climate change during the past 1000 years. Quaternary International 528, 18-29.

Swindles, G.T., Morris, P.J., Mullan, D.J., Payne, R.J., Roland, T.P., Amesbury, M.J., Lamentowicz, M., Turner, T.E., Gallego-Sala, A., Sim, T., Barr, I.D., Blaauw, M., Blundell, A., Chambers, F.M., Charman, D.J., Feurdean, A., Galloway, J.M., Gałka, M., Green, S.M., Kajukało, K., Karofeld, E., Korhola, A., Lamentowicz, Ł., Langdon, P., Marcisz, K., Mauquoy, D., Mazei, Y.A., McKeown, M.M., Mitchell, E.A.D., Novenko, E., Plunkett, G., Roe, H.M., Schoning, K., Sillasoo, Ü., Tsyganov, A.N., van der Linden, M., Väliranta, M., Warner, B., 2019. Widespread drying of European peatlands in recent centuries. Nature Geoscience 12, 922-928.

Wang, X.W., F Fu2, Pingping Qu2, Kling2, Jiang3, Y Gao1,4, and David A. Hutchins2 , Fu, F., Qu, P., Kling, J.D., Jiang, H., Gao, Y., Hutchins, D.A., 2019. How will the key marine calcifier Emiliania huxleyi respond to a warmer and more thermally variable ocean? Biogeosciences 16, 4393-4409.

Carbon Sequestration

Agartan, E., Illangasekare, T.H., Vargas-Johnson, J., Cihan, A., Birkholzer, J., 2020. Experimental investigation of assessment of the contribution of heterogeneous semi-confining shale layers on mixing and trapping of dissolved CO2 in deep geologic formations. International Journal of Greenhouse Gas Control 93, 102888.




Hassanpouryouzband, A., Yang, J., Okwananke, A., Burgass, R., Tohidi, B., Chuvilin, E., Istomin, V., Bukhanov, B., 2019. An experimental investigation on the kinetics of integrated methane recovery and CO2 sequestration by injection of flue gas into permafrost methane hydrate reservoirs. Scientific Reports 9, 16206.


Lei, H., Zhang, Q., Li, X., 2019. Preliminary numerical modeling of CO2 geological storage in the Huangcaoxia gas reservoir in the eastern Sichuan Basin, China. Geofluids 2019, 9545723.

Macquet, M., Lawton, D.C., Saeedfar, A., Osadetz, K.G., 2019. A feasibility study for detection thresholds of CO2 at shallow depths at the CaMI Field Research Station, Newell County, Alberta, Canada. Petroleum Geoscience 25, 509.

Mohajeri, M., Shariatipour, S., 2019. Evaluation of enhancing CO2 sequestration by post-brine injection under different scenarios using the E300 compositional simulator. Petroleum Research 4, 314-333.

Motie, M., Assareh, M., 2020. CO2 sequestration using carbonated water injection in depleted naturally fractured reservoirs: A simulation study. International Journal of Greenhouse Gas Control 93, 102893.

Rathnaweera, T.D., Ranjith, P.G., 2020. Nano-modified CO2 for enhanced deep saline CO2 sequestration: A review and perspective study. Earth-Science Reviews 200, 103035.

Raziperchikolaee, S., Mishra, S., 2019. Numerical simulation of CO2 huff and puff feasibility for light oil reservoirs in the Appalachian Basin: Sensitivity study and history match of a CO2 pilot test. Energy & Fuels 33, 10795-10811.

Ringrose, P.S., Meckel, T.A., 2019. Maturing global CO2 storage resources on offshore continental margins to achieve 2DS emissions reductions. Scientific Reports 9, 17944.

Slater, J.D., Chronopoulos, T., Panesar, R.S., Fitzgerald, F.D., Garcia, M., 2019. Review and techno-economic assessment of fuel cell technologies with CO2 capture. International Journal of Greenhouse Gas Control 91, 102818.

Snyder, B.F., Layne, M., Dismukes, D.E., 2020. A cash flow model of an integrated industrial CCS-EOR project in a petrochemical corridor: A case study in Louisiana. International Journal of Greenhouse Gas Control 93, 102885.

Yang, Y., Su, X., Fan, Z., Wang, D., Li, J., 2020. Numerical investigation of naphthalene deposition dynamics during CO2 leakage. International Journal of Greenhouse Gas Control 92, 102860.

Yonkofski, C., Tartakovsky, G., Huerta, N., Wentworth, A., 2019. Risk-based monitoring designs for detecting CO2 leakage through abandoned wellbores: An application of NRAP’s WLAT and DREAM tools. International Journal of Greenhouse Gas Control 91, 102807.

Coal/Lignite/Peat Geochemistry


Anwita, Ghosh, S., Varma, A.K., Das, S.K., Pal, D., Solanki, G., 2020. Metamorphic transformations of nitrogen functionalities: Stabilization of organic nitrogen in anthracite and its effect on δ15N parameter. Marine and Petroleum Geology 112, 104090.

Bullock, L., Parnell, J., Muirhead, D., Armstrong, J., Schito, A., Corrado, S., 2019. A thermal maturity map based on vitrinite reflectance of British coals. Journal of the Geological Society 176, 1136.

Garcés-Pastor, S., Wangensteen, O.S., Pérez-Haase, A., Pèlachs, A., Pérez-Obiol, R., Cañellas-Boltà, N., Mariani, S., Vegas-Vilarrúbia, T., 2019. DNA metabarcoding reveals modern and past eukaryotic communities in a high-mountain peat bog system. Journal of Paleolimnology 62, 425-441.

Li, H.-C., Wang, J., Sun, J.-J., Chou, C.-Y., Li, H.-K., Xia, Y.-Y., Zhao, H.-Y., Yang, Q.-N., Kashyap, S., 2019. Study of Jinchuan Mire in NE China I: AMS 14C, 210Pb and 137Cs dating on peat cores. Quaternary International 528, 9-17.

Li, Z., Ni, G., Sun, L., Sun, Q., Li, S., Dong, K., Xie, J., Wang, G., 2020. Effect of ionic liquid treatment on pore structure and fractal characteristics of low rank coal. Fuel 262, 116513.

Lv, D., Li, Z., Wang, D., Li, Y., Liu, H., Liu, Y., Wang, P., 2019. Sedimentary model of coal and shale in the Paleogene Lijiaya Formation of the Huangxian Basin: Insight from petrological and geochemical characteristics of coal and shale. Energy & Fuels 33, 10442-10456.

Mastalerz, M., Drobniak, A., Ames, P., McLaughlin, P.I., 2019. Application of pXRF elemental analysis and organic petrography in correlation of Pennsylvanian strata: An example from the Indiana part of the Illinois Basin, USA. International Journal of Coal Geology 216, 103342.


Moroeng, O.M., Mhuka, V., Nindi, M.M., Roberts, R.J., Wagner, N.J., 2019. Comparative study of a vitrinite-rich and an inertinite-rich Witbank coal (South Africa) using pyrolysis-gas chromatography. International Journal of Coal Science & Technology 6, 621-632.

Qi, Y., Ju, Y., Tan, J., Bowen, L., Cai, C., Yu, K., Zhu, H., Huang, C., Zhang, W., 2020. Organic matter provenance and depositional environment of marine-to-continental mudstones and coals in eastern Ordos Basin, China—Evidence from molecular geochemistry and petrology. International Journal of Coal Geology 217, 103345.

Stricker, C.A., Drexler, J.Z., Thorn, K.A., Duberstein, J.A., Rossman, S., 2019. Carbon chemistry of intact versus chronically drained peatlands in the southeastern USA. Journal of Geophysical Research: Biogeosciences 124, 2751-2767.


Vinson, D.S., Blair, N.E., Ritter, D.J., Martini, A.M., McIntosh, J.C., 2019. Carbon mass balance, isotopic tracers of biogenic methane, and the role of acetate in coal beds: Powder River Basin (USA). Chemical Geology 530, 119329.

Wu, Y., Zhu, K., Zhang, J., Müller, M., Jiang, S., Mujahid, A., Muhamad, M.F., Sia, E.S.A., 2019. Distribution and degradation of terrestrial organic matter in the sediments of peat-draining rivers, Sarawak, Malaysian Borneo. Biogeosciences 16, 4517-4533.


Zhang, Z., Wang, C., Lv, D., Hay, W.W., Wang, T., Cao, S., 2020. Precession-scale climate forcing of peatland wildfires during the early middle Jurassic greenhouse period. Global and Planetary Change 184, 103051.

COAL BED METHANE

Dai, J., Hong, F., Ni, Y., Liao, F., 2019. The positive prospect of coal-derived gas in the Yingjisu Sag, Tarim Basin, China. Journal of Natural Gas Geoscience 4, 245-255.

Qin, Y., Shen, J., Shen, Y., Li, G., Fan, B., Yao, H., 2019. Geological causes and inspirations for high production of coal measure gas in Surat Basin Acta Petrolei Sinica 40, 1147-1157.

Wang, A.K., Shao, P., 2019. Generation processes and geochemical analysis of simulated biogenic coalbed methane from lignite. Geochemistry International 57, 1295-1305.

Cosmochemistry/Planetary Geochemistry

Abplanalp, M.J., Frigge, R., Kaiser, R.I., 2019. Low-temperature synthesis of polycyclic aromatic hydrocarbons in Titan’s surface ices and on airless bodies. Science Advances 5, eaaw5841.

Clarke, J., Knightly, P., Rupert, S., 2019. Melt-water formed dark streaks on slopes of Haughton crater as possible Mars analogues. International Journal of Astrobiology 18, 518-526.

Fukushi, K., Sekine, Y., Sakuma, H., Morida, K., Wordsworth, R., 2019. Semiarid climate and hyposaline lake on early Mars inferred from reconstructed water chemistry at Gale. Nature Communications 10, 4896.

Kerraouch, I., Ebert, S., Patzek, M., Bischoff, A., Zolensky, M.E., Pack, A., Schmitt-Kopplin, P., Belhai, D., Bendaoud, A., Le, L., 2019. A light, chondritic xenolith in the Murchison (CM) chondrite – Formation by fluid-assisted percolation during metasomatism? Geochemistry 79, 125518.

King, A.J., Bates, H.C., Krietsch, D., Busemann, H., Clay, P.L., Schofield, P.F., Russell, S.S., 2019. The Yamato-type (CY) carbonaceous chondrite group: Analogues for the surface of asteroid Ryugu? Geochemistry 79, 125531.

Rapin, W., Ehlmann, B.L., Dromart, G., Schieber, J., Thomas, N.H., Fischer, W.W., Fox, V.K., Stein, N.T., Nachon, M., Clark, B.C., Kah, L.C., Thompson, L., Meyer, H.A., Gabriel, T.S.J., Hardgrove, C., Mangold, N., Rivera-Hernandez, F., Wiens, R.C., Vasavada, A.R., 2019. An interval of high salinity in ancient Gale crater lake on Mars. Nature Geoscience 12, 889-895.

Takahagi, W., Seo, K., Shibuya, T., Takano, Y., Fujishima, K., Saitoh, M., Shimamura, S., Matsui, Y., Tomita, M., Takai, K., 2019. Peptide synthesis under the alkaline hydrothermal conditions on Enceladus. ACS Earth and Space Chemistry 3, 2559-2568.

Vinogradoff, V., Le Guillou, C., Bernard, S., Viennet, J.C., Jaber, M., Remusat, L., 2020. Influence of phyllosilicates on the hydrothermal alteration of organic matter in asteroids: Experimental perspectives. Geochimica et Cosmochimica Acta 269, 150-166.

ASTROBIOLOGY

Beisbart, C., 2019. (Trans-)planetary sustainability once more – a reply to Losch. International Journal of Astrobiology 18, 590-591.

Carroll-Nellenback, J., Frank, A., Wright, J., Scharf, C., 2019. The Fermi Paradox and the aurora effect: Exo-civilization settlement, expansion, and steady states. The Astronomical Journal 158, 117.


Engler, J.-O., von Wehrden, H., 2019. ‘Where is everybody?’ An empirical appraisal of occurrence, prevalence and sustainability of technological species in the Universe. International Journal of Astrobiology 18, 495-501.

Forgan, D.H., 2019. The habitable zone for Earth-like exomoons orbiting Kepler-1625b. International Journal of Astrobiology 18, 510-517.

Forgan, D.H., 2019. Predator-prey behaviour in self-replicating interstellar probes. International Journal of Astrobiology 18, 552-561.


Gomes, A.L.S., Becker-Kerber, B., Osés, G.L., Prado, G., Becker Kerber, P., de Barros, G.E.B., Galante, D., Rangel, E., Bidola, P., Herzen, J., Pfeiffer, F., Rizzutto, M.A., Pacheco, M.L.A.F., 2019. Paleometry as a key tool to deal with paleobiological and astrobiological issues: some contributions and reflections on the Brazilian fossil record. International Journal of Astrobiology 18, 575-589.

Haezeleer, B., Böttger, U., de Vera, J.-P., Hanke, F., Fox, S., Strasdeit, H., 2019. Artifact formation during Raman measurements and its relevance to the search for chemical biosignatures on Mars. Planetary and Space Science 179, 104714.

Losch, A., 2019. Planetary sustainability: transitions of an idea. International Journal of Astrobiology 18, 592-594.

Nascimento-Dias, B.L.d., Andrade, M.B.B.d., da Costa Ludwig, Z.M., 2019. Analysing the astrobiological aspects through the comparison of pyroxenes detected in meteorites and Martian environments. International Journal of Astrobiology 18, 547-551.

Thompson, B., Burt, K., Lee, A., Lingard, K., Maurer, S.E., 2019. Partitioning of amino acids and proteins into decanol using phase transfer agents towards understanding life in non-polar liquids. Scientific Reports 9, 17750.

Wilks, J.M., Chen, F., Clark, B.C., Schneegurt, M.A., 2019. Bacterial growth in saturated and eutectic solutions of magnesium sulphate and potassium chlorate with relevance to Mars and the ocean worlds. International Journal of Astrobiology 18, 502-509.

Planetary Protection: new aspects of policy and requirements. Life Sciences in Space Research, Vol. 23, 1-142. Raulin, F., Coustenis, A., Kmienk, G., Hedman, N. (Eds.), November 2019.

Raulin, F., Coustenis, A., Kminek, G., Hedman, N., 2019. Special issue: Planetary protection: New aspects of policy and requirements. Life Sciences in Space Research 23, 1-2.

Galli, A., Losch, A., 2019. Beyond planetary protection: What is planetary sustainability and what are its implications for space research? Life Sciences in Space Research 23, 3-9.

Sterns, P.M., Tennen, L.I., 2019. Lacuna in the updated planetary protection policy and international law. Life Sciences in Space Research 23, 10-21.

Patel, N., Dean, Z., Salinas, Y., Shiraishi, L., Newlin, L., 2019. A Ground Support Biobarrier (GSB) for recontamination prevention. Life Sciences in Space Research 23, 22-30.

Gradini, R., Chen, F., Tan, R., Newlin, L., 2019. A summary on cutting edge advancements in sterilization and cleaning technologies in medical, food, and drug industries, and its applicability to spacecraft hardware. Life Sciences in Space Research 23, 31-49.

Meyer, M., Bakermans, C., Beaty, D., Bernard, D., Boston, P., Chevrier, V., Conley, C., Feustel, I., Gough, R., Glotch, T., Hays, L., Junge, K., Lindberg, R., Mellon, M., Mischna, M., Neal, C.R., Pugel, B., Quinn, R., Raulin, F., Rennó, N., Rummel, J., Schulte, M., Spry, A., Stabekis, P., Wang, A., Yee, N., 2019. Report of the Joint Workshop on Induced Special Regions. Life Sciences in Space Research 23, 50-59.

Rummel, J.D., Pugel, D.E., 2019. Planetary protection technologies for planetary science instruments, spacecraft, and missions: Report of the NASA Planetary Protection Technology Definition Team (PPTDT). Life Sciences in Space Research 23, 60-68.

Viso, M., 2019. Mars sample receiving facility or facilities? That is the question. Life Sciences in Space Research 23, 69-72.

Fujita, K., Kurosawa, K., Genda, H., Hyodo, R., Matsuyama, S., Yamagishi, A., Mikouchi, T., Niihara, T., 2019. Assessment of the probability of microbial contamination for

sample return from Martian moons I: Departure of microbes from Martian surface. Life Sciences in Space Research 23, 73-84.

Kurosawa, K., Genda, H., Hyodo, R., Yamagishi, A., Mikouchi, T., Niihara, T., Matsuyama, S., Fujita, K., 2019. Assessment of the probability of microbial contamination for sample return from Martian moons II: The fate of microbes on Martian moons. Life Sciences in Space Research 23, 85-100.

Patel, M.R., Pearson, V.K., Evans, D.J., Summers, D.J., Paton, S., Truscott, P., Pottage, T., Bennett, A., Gow, J.P.D., Goodyear, M.D., Mason, J.P., Leese, M.R., Patel, R.D., 2019. The transfer of unsterilized material from Mars to Phobos: Laboratory tests, modelling and statistical evaluation. Life Sciences in Space Research 23, 112-134.

Summers, D., 2019. Modelling the transfer of life from Mars to its moons. Life Sciences in Space Research 23, 101-111.

Smith, D.H., Detsis, E., 2019. Planetary protection classification of samples returned from the martian moons: Summary of a review by the European Science Foundation and the National Academies of Sciences, Engineering and Medicine. Life Sciences in Space Research 23, 135-140.

Environmental Geochemistry

Ahmed, O.E., Eldesoky, A.M., El Nady, M.M., 2019. Evaluation of petroleum hydrocarbons and its impact on organic matters of living organisms in the northwestern Gulf of Suez, Egypt. Petroleum Science and Technology 37, 2441-2449.

Amin, J.S., Kuyakhi, H.R., Bahadori, A., 2019. Intelligent prediction of aliphatic and aromatic hydrocarbons in Caspian Sea sediment using a neural network based on particle swarm optimization. Petroleum Science and Technology 37, 2364-2373.



Gadelha, L.G., Frena, M., Damasceno, F.C., Santos, E., SantÀnna, M.V.S., Vinhas, M.A., Barreto, T.S.A., Alexandre, M.R., 2019. Distribution patterns of aliphatic hydrocarbons in sediments from a tropical estuarine system. Marine Pollution Bulletin 149, 110607.

Hughes, S.A., Naile, J., Pinza, M., Ray, C., Hester, B., Baum, J., Gardiner, W., Kallestad, W., Brzuzy, L., 2019. Characterization of miscellaneous effluent discharges from a mobile offshore drilling unit to the marine environment. Environmental Toxicology and Chemistry 38, 2811-2823.

Humez, P., Osselin, F., Wilson, L.J., Nightingale, M., Kloppmann, W., Mayer, B., 2019. A probabilistic approach for predicting methane occurrence in groundwater. Environmental Science & Technology 53, 12914-12922.

Veldkornet, D., Rajkaran, A., Paul, S., Naidoo, G., 2020. Oil induces chlorophyll deficient propagules in mangroves. Marine Pollution Bulletin 150, 110667.

Wang, L., Liu, H., Chen, S., Wang, M., Liu, Y., Yu, W., Zhang, X., 2019. Crude oil-contaminated soil treatment and oil recovery through micro-emulsion washing. Energy & Fuels 33, 11486-11493.

Wen, D., Ordonez, D., Valencia, A., McKenna, A.M., Chang, N.-B., 2020. Copper impact on enzymatic cascade and extracellular sequestration via distinctive pathways of nitrogen removal in green sorption media at varying stormwater field conditions. Chemosphere 243, 125399.

Winding, A., Modrzyński, J.J., Christensen, J.H., Brandt, K.K., Mayer, P., 2019. Soil bacteria and protists show different sensitivity to polycyclic aromatic hydrocarbons at controlled chemical activity. FEMS Microbiology Letters 366.

Wirth, M.A., Sievers, M., Habedank, F., Kragl, U., Schulz-Bull, D.E., Kanwischer, M., 2019. Electrodialysis as a sample processing tool for bulk organic matter and target pollutant analysis of seawater. Marine Chemistry 217, 103719.


Zhao, Y., Wang, L., Luo, J., Huang, T., Tao, S., Liu, J., Yu, Y., Huang, Y., Liu, X., Ma, J., 2019. Deep learning prediction of polycyclic aromatic hydrocarbons in the high Arctic. Environmental Science & Technology 53, 13238-13245.

BIOREMEDIATION


Khomarbaghi, Z., Shavandi, M., Amoozegar, M.A., Dastgheib, S.M.M., 2019. Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study. International Journal of Environmental Science and Technology 16, 7849-7860.


Soares-Castro, P., Yadav, T.C., Viggor, S., Kivisaar, M., Kapley, A., Santos, P.M., 2019. Seasonal bacterial community dynamics in a crude oil refinery wastewater treatment plant. Applied Microbiology and Biotechnology 103, 9131-9141.

Vergeynst, L., Greer, C.W., Mosbech, A., Gustavson, K., Meire, L., Poulsen, K.G., Christensen, J.H., 2019. Biodegradation, photo-oxidation, and dissolution of petroleum

compounds in an Arctic fjord during summer. Environmental Science & Technology 53, 12197-12206.

Wegeberg, S., Hansson, S.V., van Beest, F.M., Fritt-Rasmussen, J., Gustavson, K., 2020. Smooth or smothering? The self-cleaning potential and photosynthetic effects of oil spill on arctic macro-algae Fucus distichus. Marine Pollution Bulletin 150, 110604.

DEEPWATER HORIZON /MACONDO/OTHER OIL SPILLS


Egres, A.G., Hatje, V., Gallucci, F., Machado, M.E., Barros, F., 2019. Effects of an experimental oil spill on the structure and function of benthic assemblages with different history of exposure to oil perturbation. Marine Environmental Research 152, 104822.

Nandimandalam, H., Gude, V.G., 2019. Indigenous biosensors for in situ hydrocarbon detection in aquatic environments. Marine Pollution Bulletin 149, 110643.

Pančić, M., Köhler, E., Paulsen, M.L., Toxværd, K., Lacroix, C., Le Floch, S., Hjorth, M., Nielsen, T.G., 2019. Effects of oil spill response technologies on marine microorganisms in the high Arctic. Marine Environmental Research 151, 104785.

Quist, A.J.L., Rohlman, D.S., Kwok, R.K., Stewart, P.A., Stenzel, M.R., Blair, A., Miller, A.K., Curry, M.D., Sandler, D.P., Engel, L.S., 2019. Deepwater Horizon oil spill exposures and neurobehavioral function in Gulf study participants. Environmental Research 179, 108834.

Rohal, M., Barrera, N., Van Eenennaam, J.S., Foekema, E.M., Montagna, P.A., Murk, A.J., Pryor, M., Romero, I.C., 2020. The effects of experimental oil-contaminated marine snow on meiofauna in a microcosm. Marine Pollution Bulletin 150, 110656.

Snyder, S.M., Pulster, E.L., Murawski, S.A., 2019. Associations between chronic exposure to polycyclic aromatic hydrocarbons and health indices in Gulf of Mexico tilefish (Lopholatilus chamaeleonticeps) post Deepwater Horizon. Environmental Toxicology and Chemistry 38, 2659-2671.

Stoyanovich, S.S., Yang, Z., Hanson, M., Hollebone, B.P., Orihel, D.M., Palace, V., Rodriguez-Gil, J.L., Faragher, R., Mirnaghi, F.S., Shah, K., Blais, J.M., 2019. Simulating a spill of diluted bitumen: Environmental weathering and submergence in a model freshwater system. Environmental Toxicology and Chemistry 38, 2621-2628.

Struch, R.E., Pulster, E.L., Schreier, A.D., Murawski, S.A., 2019. Hepatobiliary analyses suggest chronic PAH exposure in hakes (Urophycis spp.) following the Deepwater Horizon oil spill. Environmental Toxicology and Chemistry 38, 2740-2749.



Yaghmour, F., 2019. Are oil spills a key mortality factor for marine turtles from the eastern coast of the United Arab Emirates? Marine Pollution Bulletin 149, 110624.

Zhou, Z., Li, X., Chen, L., Li, B., Wang, C., Guo, J., Shi, P., Yang, L., Liu, B., Song, B., 2019. Effects of diesel oil spill on macrobenthic assemblages at the intertidal zone: A mesocosm experiment in situ. Marine Environmental Research 152, 104823.

MICROPLASTICS

Dierkes, G., Lauschke, T., Becher, S., Schumacher, H., Földi, C., Ternes, T., 2019. Quantification of microplastics in environmental samples via pressurized liquid extraction and pyrolysis-gas chromatography. Analytical and Bioanalytical Chemistry 411, 6959-6968.

Liu, P., Zhan, X., Wu, X., Li, J., Wang, H., Gao, S., 2020. Effect of weathering on environmental behavior of microplastics: Properties, sorption and potential risks. Chemosphere 242, 125193.

Peñalver, R., Arroyo-Manzanares, N., López-García, I., Hernández-Córdoba, M., 2020. An overview of microplastics characterization by thermal analysis. Chemosphere 242, 125170.

Xu, S., Ma, J., Ji, R., Pan, K., Miao, A.-J., 2020. Microplastics in aquatic environments: Occurrence, accumulation, and biological effects. Science of The Total Environment 703, 134699.

OIL SAND PROCESS WATERS/TAILING PONDS


Eccles, K.M., Pauli, B.D., Chan, H.M., 2019. The use of geographic information systems for spatial ecological risk assessments: An example from the Athabasca oil sands area in Canada. Environmental Toxicology and Chemistry 38, 2797-2810.

Evolution/Paleontology/Palynology

Álvaro, J.J., Cortijo, I., Jensen, S., Martí Mus, M., Palacios, T., 2020. Cloudina-microbial reef resilience to substrate instability in a Cadomian retro-arc basin of the Iberian Peninsula. Precambrian Research 336, 105479.

Boatman, E.M., Goodwin, M.B., Holman, H.-Y.N., Fakra, S., Zheng, W., Gronsky, R., Schweitzer, M.H., 2019. Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex. Scientific Reports 9, 15678.


Virtual Palaeontology: when fossils reconstructed by X-ray tomography. Paleoworld, 29(4), 425-576. Edited by Zong-Jun Yin, Jing Lu


Huang, J.-Y., Martínez-Pérez, C., Hu, S.-X., Donoghue, P.C.J., Zhang, Q.-Y., Zhou, C.-Y., Wen, W., Benton, M.J., Luo, M., Yao, H.-Z., Zhang, K.-X., 2019. Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography. Palaeoworld 28, 429-440.

Gai, Z.-K., Zhu, M., Donoghue, P.C.J., 2019. The circulatory system of Galeaspida (Vertebrata; stem-Gnathostomata) revealed by synchrotron X-ray tomographic microscopy. Palaeoworld 28, 441-460.

Landon, E.N.U., Liu, P.-J., Yin, Z.-J., Sun, W.-C., Shang, X.-D., Donoghue, P.C.J., 2019. Cellular preservation of excysting developmental stages of new eukaryotes from the early Ediacaran Weng’an Biota. Palaeoworld 28, 461-468.

Sun, W.-C., Yin, Z.-J., Donoghue, P., Liu, P.-J., Shang, X.-D., Zhu, M.-Y., 2019. Tubular microfossils from the Ediacaran Weng’an Biota (Doushantuo Formation, South China) are not early animals. Palaeoworld 28, 469-477.

Shi, Y.-K., Huang, H., Shen, Z.-H., 2019. New insights for ancient foraminifera through 3D visuals of fusulinids. Palaeoworld 28, 478-486.

Li, D.-D., Wang, J., Wan, S., Pšenička, J., Zhou, W.-M., Bek, J., Votočková-Frojdová, J., 2019. A marattialean fern, Scolecopteris libera n. sp., from the Asselian (Permian) of Inner Mongolia, China. Palaeoworld 28, 487-507.

Yu, T.-T., Wang, B., Jarzembowski, E., 2019. First record of marine gastropods (wentletraps) from mid-Cretaceous Burmese amber. Palaeoworld 28, 508-513.

Wang, Y.-Y., Wang, X.-Q., Hu, B., Luo, M., 2019. Tomographic reconstructions of crab burrows from deltaic tidal flat: Contribution to palaeoecology of decapod trace fossils in coastal settings. Palaeoworld 28, 514-524.

Hu, Y.-Z., Young, G.C., Burrow, C., Zhu, Y.-a., Lu, J., 2019. High resolution XCT scanning reveals complex morphology of gnathal elements in an Early Devonian arthrodire. Palaeoworld 28, 525-534.

Hu, Y.-Z., Young, G.C., Lu, J., 2019. The Upper Devonian tetrapodomorph Gogonasus andrewsae from Western Australia: Reconstruction of the shoulder girdle and opercular series using X-ray Micro-Computed Tomography. Palaeoworld 28, 535-542.

Lu, J., Zhu, M., 2019. The postparietal shield of the Pragian dipnomorph Arquatichthys and its implications for the rhipidistian cranial anatomy. Palaeoworld 28, 543-549.

Yi, H., Norell, M., 2019. The bony labyrinth of Platecarpus (Squamata: Mosasauria) and aquatic adaptations in squamate reptiles. Palaeoworld 28, 550-561.

Li, Z.-H., Yan, F., Ketcham, R.A., Colbert, M.W., Clarke, J.A., 2019. Mass-transfer based modeling to investigate iodine staining effects for enhanced contrast X-ray computed tomography. Palaeoworld 28, 562-571.

Clapham, M.E., 2019. Conservation evidence from climate-related stressors in the deep-time marine fossil record. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190223.


Harper, D.A.T., Hammarlund, E.U., Topper, T.P., Nielsen, A.T., Rasmussen, J.A., Park, T.-Y.S., Smith, M.P., 2019. The Sirius Passet Lagerstätte of North Greenland: a remote window on the Cambrian Explosion. Journal of the Geological Society 176, 1023.

Korasidis, V.A., Wagstaff, B.E., 2020. The rise of flowering plants in the high southern latitudes of Australia. Review of Palaeobotany and Palynology 272, 104126.

Luque, J., Gerken, S., 2019. Exceptional preservation of comma shrimp from a mid-Cretaceous Lagerstätte of Colombia, and the origins of crown Cumacea. Proceedings of the Royal Society B: Biological Sciences 286, 20191863.

Penny, A., Kröger, B., 2019. Impacts of spatial and environmental differentiation on early Palaeozoic marine biodiversity. Nature Ecology & Evolution 3, 1655-1660.

Pereira, R., Lima, F.J.d., Simbras, F.M., Bittar, S.M.B., Kellner, A.W.A., Saraiva, A.Á.F., Bantim, R.A.M., Sayão, J.M., Oliveira, G.R., 2020. Biomarker signatures of Cretaceous Gondwana amber from Ipubi Formation (Araripe Basin, Brazil) and their palaeobotanical significance. Journal of South American Earth Sciences 98, 102413.


Schoenemann, B., Poschmann, M., Clarkson, E.N.K., 2019. Insights into the 400 million-year-old eyes of giant sea scorpions (Eurypterida) suggest the structure of Palaeozoic compound eyes. Scientific Reports 9, 17797.

Sheldon, N.D., Smith, S.Y., Stein, R., Ng, M., 2020. Carbon isotope ecology of gymnosperms and implications for paleoclimatic and paleoecological studies. Global and Planetary Change 184, 103060.

ORIGINS OF LIFE/MICROBIAL GENOMICS

Adam, P.S., Borrel, G., Gribaldo, S., 2019. An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. Nature Microbiology 4, 2155-2163.

Bhowmik, S., Krishnamurthy, R., 2019. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nature Chemistry 11, 1009-1018.

Catchpole, R.J., Forterre, P., 2019. The evolution of reverse gyrase suggests a nonhyperthermophilic last universal common ancestor. Molecular Biology and Evolution 36, 2737-2747.

Demongeot, J., Seligmann, H., 2019. The Uroboros theory of life’s origin: 22-nucleotide theoretical minimal RNA rings reflect evolution of genetic code and tRNA-rRNA translation machineries. Acta Biotheoretica 67, 273-297.

Goldford, J.E., Hartman, H., Marsland, R., Segrè, D., 2019. Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. Nature Ecology & Evolution 3, 1715-1724.

Iqubal, M.A., Sharma, R., Kamaluddin, Jheeta, S., 2019. Synthesis of nucleic acid bases by metal ferrite nanoparticles from a single carbon atom precursor molecule: Formamide. Origins of Life and Evolution of Biospheres 49, 147-162.

Jordan, S.F., Rammu, H., Zheludev, I.N., Hartley, A.M., Maréchal, A., Lane, N., 2019. Promotion of protocell self-assembly from mixed amphiphiles at the origin of life. Nature Ecology & Evolution 3, 1705-1714.

Lavado, N., de la Concepción, J.G., Babiano, R., Cintas, P., Light, M.E., 2019. Interactions of amino acids and aminoxazole derivatives: Cocrystal formation and prebiotic implications enabled by computational analysis. Origins of Life and Evolution of Biospheres 49, 163-185.

Lingam, M., Loeb, A., 2019. Role of stellar physics in regulating the critical steps for life. International Journal of Astrobiology 18, 527-546.

Mariscal, C., Barahona, A., Aubert-Kato, N., Aydinoglu, A.U., Bartlett, S., Cárdenas, M.L., Chandru, K., Cleland, C., Cocanougher, B.T., Comfort, N., Cornish-Bowden, A., Deacon, T., Froese, T., Giovannelli, D., Hernlund, J., Hut, P., Kimura, J., Maurel, M.-C., Merino, N., Moreno, A., Nakagawa, M., Peretó, J., Virgo, N., Witkowski, O., Cleaves, H.J., 2019. Hidden concepts in the history and philosophy of origins-of-life studies: A workshop report. Origins of Life and Evolution of Biospheres 49, 111-145.

Obata, D., Takabayashi, A., Tanaka, R., Tanaka, A., Ito, H., 2019. Horizontal transfer of promiscuous activity from nonphotosynthetic bacteria contributed to evolution of chlorophyll degradation pathway. Molecular Biology and Evolution 36, 2830-2841.

Stovbun, S.V., Zanin, A.M., Shashkov, M.V., Skoblin, A.A., Zlenko, D.V., Tverdislov, V.A., Mikhaleva, M.G., Taran, O.P., Parmon, V.N., 2019. Spontaneous resolution and super-coiling in xerogels of the products of photo-induced formose reaction. Origins of Life and Evolution of Biospheres 49, 187-196.



Tsaousis, A.D., 2019. On the origin of iron/sulfur cluster biosynthesis in eukaryotes. Frontiers in Microbiology 10, 2478. doi: 2410.3389/fmicb.2019.02478.

Weiner, I., Shahar, N., Marco, P., Yacoby, I., Tuller, T., 2019. Solving the riddle of the evolution of Shine-Dalgarno based translation in chloroplasts. Molecular Biology and Evolution 36, 2854-2860.

HOMINID EVOLUTION

Böhme, M., Spassov, N., Fuss, J., Tröscher, A., Deane, A.S., Prieto, J., Kirscher, U., Lechner, T., Begun, D.R., 2019. A new Miocene ape and locomotion in the ancestor of great apes and humans. Nature 575, 489-493.

Brittingham, A., Hren, M.T., Hartman, G., Wilkinson, K.N., Mallol, C., Gasparyan, B., Adler, D.S., 2019. Geochemical evidence for the control of fire by Middle Palaeolithic hominins. Scientific Reports 9, 15368.

Colbran, L.L., Gamazon, E.R., Zhou, D., Evans, P., Cox, N.J., Capra, J.A., 2019. Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Nature Ecology & Evolution 3, 1598-1606.

Connolly, R., Jambrina-Enríquez, M., Herrera-Herrera, A.V., Vidal-Matutano, P., Fagoaga, A., Marquina-Blasco, R., Marin-Monfort, M.D., Ruiz-Sánchez, F.J., Laplana, C., Bailon, S., Pérez, L., Leierer, L., Hernández, C.M., Galván, B., Mallol, C., 2019. A multiproxy record of palaeoenvironmental conditions at the Middle Palaeolithic site of Abric del Pastor (Eastern Iberia). Quaternary Science Reviews 225, 106023.

Greenbaum, G., Getz, W.M., Rosenberg, N.A., Feldman, M.W., Hovers, E., Kolodny, O., 2019. Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nature Communications 10, 5003.

Kivell, T.L., 2019. Fossil ape hints at how walking on two feet evolved. Nature 575, 445-466.

Medin, T., Martínez-Navarro, B., Madurell-Malapeira, J., Figueirido, B., Kopaliani, G., Rivals, F., Kiladze, G., Palmqvist, P., Lordkipanidze, D., 2019. The bears from Dmanisi and the first dispersal of early Homo out of Africa. Scientific Reports 9, 17752.

Warren, J.L.A., Ponce de León, M.S., Hopkins, W.D., Zollikofer, C.P.E., 2019. Evidence for independent brain and neurocranial reorganization during hominin evolution. Proceedings of the National Academy of Sciences 116, 22115-22121.

Yan, S.M., McCoy, R.C., 2019. Functional divergence among hominins. Nature Ecology & Evolution 3, 1507-1508.

Fluid Inclusions

Frezzotti, M.L., 2019. Diamond growth from organic compounds in hydrous fluids deep within the Earth. Nature Communications 10, 4952.

Kempton, R.H., Bourdet, J., Gong, S., Ross, A.S., 2020. Revealing oil migration in the frontier Bight Basin, Australia. Marine and Petroleum Geology 113, 104124.

Kinoshita, M., Ijiri, A., Haraguchi, S., Jiménez-Espejo, F.J., Komai, N., Suga, H., Sugihara, T., Tanikawa, W., Hirose, T., Hamada, Y., Gupta, L.P., Ahagon, N., Masaki, Y., Abe, N., Wu, H.Y., Nomura, S., Lin, W., Yamamoto, Y., Yamada, Y., 2019. Constraints on the fluid supply rate into and through gas hydrate reservoir systems as inferred from pore-water chloride and in situ temperature profiles, Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 368-376.

Saade, M., Araragi, K., Montagner, J.P., Kaminski, E., Roux, P., Aoki, Y., Brenguier, F., 2019. Evidence of reactivation of a hydrothermal system from seismic anisotropy changes. Nature Communications 10, 5278.

Wang, Y., Chang, X., Sun, Y., Shi, B., Qin, S., 2020. Investigation of fluid inclusion and oil geochemistry to delineate the charging history of Upper Triassic Chang 6, Chang 8, and Chang 9 tight oil reservoirs, Southeastern Ordos Basin, China. Marine and Petroleum Geology 113, 104115.

Wen, S., Liu, J., Deng, J., 2019. Fluid Inclusion Effect in Flotation of Sulfide Minerals. Elsevier. 246 pp.

General Interest

Akri, M., Zhao, S., Li, X., Zang, K., Lee, A.F., Isaacs, M.A., Xi, W., Gangarajula, Y., Luo, J., Ren, Y., Cui, Y.-T., Li, L., Su, Y., Pan, X., Wen, W., Pan, Y., Wilson, K., Li, L., Qiao, B., Ishii, H., Liao, Y.-F., Wang, A., Wang, X., Zhang, T., 2019. Atomically dispersed nickel as coke-resistant active sites for methane dry reforming. Nature Communications 10, 5181.

Erhard, A., Wallman, J.J., Postler, L., Meth, M., Stricker, R., Martinez, E.A., Schindler, P., Monz, T., Emerson, J., Blatt, R., 2019. Characterizing large-scale quantum computers via cycle benchmarking. Nature Communications 10, 5347.

Fillinger, S., de la Garza, L., Peltzer, A., Kohlbacher, O., Nahnsen, S., 2019. Challenges of big data integration in the life sciences. Analytical and Bioanalytical Chemistry 411, 6791-6800.

Liu, D., Zhang, P., Chen, D., Howell, K., 2019. From the vineyard to the winery: How microbial ecology drives regional distinctiveness of wine. Frontiers in Microbiology 10, 2679. doi: 2610.3389/fmicb.2019.02679.

Lombardi, F., Lodi, A., Ma, J., Liu, J., Slota, M., Narita, A., Myers, W.K., Müllen, K., Feng, X., Bogani, L., 2019. Quantum units from the topological engineering of molecular graphenoids. Science 366, 1107-1110.


Wu, Y., Jiang, Z., Lu, X., Liang, Y., Wang, H., 2019. Domino electroreduction of CO2 to methanol on a molecular catalyst. Nature 575, 639-642.

Geology

Bärenbold, F., Schmid, M., Brennwald, M.S., Kipfer, R., 2020. Missing atmospheric noble gases in a large, tropical lake: The case of Lake Kivu, East-Africa. Chemical Geology 532, 119374.

Estes, E.R., Berti, D., Coffey, N.R., Hochella, M.F., Wozniak, A.S., Luther, G.W., 2019. Abiotic synthesis of graphite in hydrothermal vents. Nature Communications 10, 5179.


Gillman, M., Erenler, H., 2019. Reconciling the Earth's stratigraphic record with the structure of our galaxy. Geoscience Frontiers 10, 2147-2151.

Gu, X., Rempe, D.M., Dietrich, W.E., West, A.J., Lin, T.-C., Jin, L., Brantley, S.L., 2020. Chemical reactions, porosity, and microfracturing in shale during weathering: The effect of erosion rate. Geochimica et Cosmochimica Acta 269, 63-100.

Hirslund, F., Morkel, P., 2020. Managing the dangers in Lake Kivu – How and why. Journal of African Earth Sciences 161, 103672.

Le Pichon, X., Şengör, A.M.C., İmren, C., 2019. Pangea and the lower mantle. Tectonics 38, 3479-3504.



BOLIDE IMPACTS/CRATER GEOCHEMISTRY

Nozaki, T., Ohta, J., Noguchi, T., Sato, H., Ishikawa, A., Takaya, Y., Kimura, J.-I., Chang, Q., Shimada, K., Ishibashi, J.-i., Yasukawa, K., Kimoto, K., Iijima, K., Kato, Y., 2019. A Miocene impact ejecta layer in the pelagic Pacific Ocean. Scientific Reports 9, 16111.


Hydrates

Braga, R., Iglesias, R.S., Romio, C., Praeg, D., Miller, D.J., Viana, A., Ketzer, J.M., 2020. Modelling methane hydrate stability changes and gas release due to seasonal oscillations in bottom water temperatures on the Rio Grande cone, offshore southern Brazil. Marine and Petroleum Geology 112, 104071.


Lei, L., Seol, Y., Myshakin, E.M., 2019. Methane hydrate film thickening in porous media. Geophysical Research Letters 46, 11091-11099.

Liang, J., Zhang, W., Lu, J.a., Wei, J., Kuang, Z., He, Y., 2019. Geological occurrence and accumulation mechanism of natural gas hydrates in the eastern Qiongdongnan Basin of the South China Sea: Insights from site GMGS5-W9-2018. Marine Geology 418, 106042.

Liu, X., Liu, C., Wu, J., 2019. Dynamic characteristics of offshore natural gas hydrate dissociation by depressurization in marine sediments. Geofluids 2019, 6074892.

Shi, Y.-h., Liang, Q.-y., Yang, J.-p., Yuan, Q.-m., Wu, X.-m., Kong, L., 2019. Stability analysis of submarine slopes in the area of the test production of gas hydrate in the South China Sea. China Geology 2, 276-286.

Sun, H., Chen, B., Yang, M., 2020. Effect of multiphase flow on natural gas hydrate production in marine sediment. Journal of Natural Gas Science and Engineering 73, 103066.

Van de Wetering, N., Esterle, J.S., Golding, S.D., Rodrigues, S., Götz, A.E., 2019. Carbon isotopic evidence for rapid methane clathrate release recorded in coals at the terminus of the Late Palaeozoic Ice Age. Scientific Reports 9, 16544.


Zhang, W., Liang, J., Su, P., Wei, J., Gong, Y., Lin, L., Liang, J., Huang, W., 2019. Distribution and characteristics of mud diapirs, gas chimneys, and bottom simulating reflectors associated with hydrocarbon migration and gas hydrate accumulation in the Qiongdongnan Basin, northern slope of the South China Sea. Geological Journal 54, 3556-3573.

Marine Gas Hydrate Reservoir Systems along the Eastern Continental Margin of India: Results of the National Gas Hydrate Program Expedition 02. Marine and Petroleum Geology 108, 1-746. October 2019. Collett, T.S, Pratap, M., Singh, S.K., Chopra, K.K, Kumar, P., Yamada, Y., Tenma, N., Sain, K., Sahay, U.S., Boswell, R., Waite, W.

Collett, T.S., Kumar, P., Boswell, R., Waite, W.F., 2019. Preface: Marine gas hydrate reservoir systems along the Eastern Continental Margin of India: Results of the National Gas Hydrate Program Expedition 02. Marine and Petroleum Geology 108, 1-2.

Kumar, P., Collett, T.S., Shukla, K.M., Yadav, U.S., Lall, M.V., Vishwanath, K., 2019. India National Gas Hydrate Program Expedition-02: Operational and technical summary. Marine and Petroleum Geology 108, 3-38.

Collett, T.S., Boswell, R., Waite, W.F., Kumar, P., Roy, S.K., Chopra, K., Singh, S.K., Yamada, Y., Tenma, N., Pohlman, J., Zyrianova, M., 2019. India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Gas hydrate systems along the eastern continental margin of India. Marine and Petroleum Geology 108, 39-142.

Boswell, R., Yoneda, J., Waite, W.F., 2019. India National Gas Hydrate Program Expedition 02 summary of scientific results: Evaluation of natural gas-hydrate-bearing pressure cores. Marine and Petroleum Geology 108, 143-153.

Boswell, R., Myshakin, E., Moridis, G., Konno, Y., Collett, T.S., Reagan, M., Ajayi, T., Seol, Y., 2019. India National Gas Hydrate Program Expedition 02 summary of scientific results: Numerical simulation of reservoir response to depressurization. Marine and Petroleum Geology 108, 154-166.

Shukla, K.M., Collett, T.S., Kumar, P., Yadav, U.S., Boswell, R., Frye, M., Riedel, M., Kaur, I., Vishwanath, K., 2019. National Gas Hydrate Program expedition 02: Identification of gas hydrate prospects in the Krishna-Godavari Basin, offshore India. Marine and Petroleum Geology 108, 167-184.

Shukla, K.M., Kumar, P., Yadav, U.S., 2019. Gas hydrate reservoir identification, delineation, and characterization in the Krishna-Godavari basin using subsurface geologic and geophysical data from the National Gas Hydrate Program 02 Expedition, offshore India. Marine and Petroleum Geology 108, 185-205.

Hsiung, K.-H., Saito, S., Kanamatsu, T., Sanada, Y., Yamada, Y., 2019. Regional stratigraphic framework and gas hydrate occurrence offshore eastern India: Core-log-seismic integration of National Gas Hydrate Program Expedition 02 (NGHP-02) Area-B drill sites. Marine and Petroleum Geology 108, 206-215.

Saito, S., Hsiung, K.-H., Sanada, Y., Moe, K., Hamada, Y., Nakamura, Y., Wu, H.-Y., Shinmoto, Y., Yamada, Y., 2019. Gas hydrate occurrence and distribution controlled by regional geological structure off eastern India: Estimates from logging-while-drilling in Area-B, National Gas Hydrate Program Expedition 02 (NGHP-02). Marine and Petroleum Geology 108, 216-225.

Nanda, J., Shukla, K.M., Lall, M.V., Yadav, U.S., Kumar, P., 2019. Lithofacies characterization of gas hydrate prospects discovered during the National Gas Hydrate Program expedition 02, offshore Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 226-238.


Jang, J., Waite, W.F., Stern, L.A., Collett, T.S., Kumar, P., 2019. Physical property characteristics of gas hydrate-bearing reservoir and associated seal sediments collected during NGHP-02 in the Krishna-Godavari Basin, in the offshore of India. Marine and Petroleum Geology 108, 249-271.

Waite, W.F., Jang, J., Collett, T.S., Kumar, P., 2019. Downhole physical property-based description of a gas hydrate petroleum system in NGHP-02 Area C: A channel, levee, fan complex in the Krishna-Godavari Basin offshore eastern India. Marine and Petroleum Geology 108, 272-295.

Waite, W.F., Ruppel, C.D., Collett, T.S., Schultheiss, P., Holland, M., Shukla, K.M., Kumar, P., 2019. Multi-measurement approach for establishing the base of gas hydrate occurrence in the Krishna-Godavari Basin for sites cored during expedition NGHP-02 in the offshore of India. Marine and Petroleum Geology 108, 296-320.

Muraoka, M., Ohtake, M., Susuki, N., Morita, H., Oshima, M., Yamamoto, Y., 2019. Thermal properties of highly saturated methane hydrate-bearing sediments recovered from the Krishna–Godavari Basin. Marine and Petroleum Geology 108, 321-331.

Tanikawa, W., Hirose, T., Hamada, Y., Gupta, L.P., Ahagon, N., Masaki, Y., Abe, N., Wu, H.Y., Sugihara, T., Nomura, S., Lin, W., Kinoshita, M., Yamamoto, Y., Yamada, Y., 2019. Porosity, permeability, and grain size of sediment cores from gas-hydrate-bearing sites and their implication for overpressure in shallow argillaceous formations: Results from the national gas hydrate program expedition 02, Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 332-347.

Hirose, T., Tanikawa, W., Hamada, Y., Lin, W., Hatakeda, K., Tadai, O., Wu, H.Y., Nomura, S., Abe, N., Gupta, L.P., Sugihara, T., Masaki, Y., Kinoshita, M., Yamada, Y., 2019. Strength characteristics of sediments from a gas hydrate deposit in the Krishna–Godavari Basin on the eastern margin of India. Marine and Petroleum Geology 108, 348-355.

Hamada, Y., Hirose, T., Saito, S., Moe, K., Wu, H., Tanikawa, W., Sanada, Y., Nakamura, Y., Shimmoto, Y., Sugihara, T., Lin, W., Abe, N., Gupta, L., Kinoshita, M., Masaki, Y., Nomura, S., Yamada, Y., 2019. Equivalent formation strength as a proxy tool for exploring for the location and distribution of gas hydrates. Marine and Petroleum Geology 108, 356-367.

Kinoshita, M., Ijiri, A., Haraguchi, S., Jiménez-Espejo, F.J., Komai, N., Suga, H., Sugihara, T., Tanikawa, W., Hirose, T., Hamada, Y., Gupta, L.P., Ahagon, N., Masaki, Y., Abe, N., Wu, H.Y., Nomura, S., Lin, W., Yamamoto, Y., Yamada, Y., 2019. Constraints on the fluid supply rate into and through gas hydrate reservoir systems as inferred from pore-

water chloride and in situ temperature profiles, Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 368-376.

Ijiri, A., Haraguchi, S., Jiménez-Espejo, F.J., Komai, N., Suga, H., Kinoshita, M., Inagaki, F., Yamada, Y., 2019. Origin of low-chloride fluid in sediments from the eastern continental margin of India, results from the National Gas Hydrate Program Expedition 02. Marine and Petroleum Geology 108, 377-388.

Dixit, G., Ram, H., Kumar, P., 2019. Origin of gas in gas hydrates as interpreted from geochemistry data obtained during the National Gas Hydrate Program Expedition 02, Krishna Godavari Basin, offshore India. Marine and Petroleum Geology 108, 389-396.

Tripathi, R., Kumar, P., Ghosh, S., Nagalingam, J., Singh, H., 2019. Culture based investigations of key microbial functional groups in gas hydrate bearing sediments of the Krishna-Godavari Basin in offshore India. Marine and Petroleum Geology 108, 397-406.


Priest, J.A., Hayley, J.L., Smith, W.E., Schultheiss, P., Roberts, J., 2019. PCATS triaxial testing: Geomechanical properties of sediments from pressure cores recovered from the Bay of Bengal during expedition NGHP-02. Marine and Petroleum Geology 108, 424-438.


Kida, M., Jin, Y., Yoneda, J., Oshima, M., Kato, A., Konno, Y., Nagao, J., Tenma, N., 2019. Crystallographic and geochemical properties of natural gas hydrates accumulated in the National Gas Hydrate Program Expedition 02 drilling sites in the Krishna-Godavari Basin off India. Marine and Petroleum Geology 108, 471-481.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Jang, J., Waite, W.F., Kumar, P., Tenma, N., 2019. Pressure core based onshore laboratory analysis on mechanical properties of hydrate-bearing sediments recovered during India's National Gas Hydrate Program Expedition (NGHP) 02. Marine and Petroleum Geology 108, 482-501.

Kato, A., Konno, Y., Yoneda, J., Kida, M., Oshima, M., Jin, Y., Nagao, J., Tenma, N., 2019. Evaluation of failure modes and undrained shear strength by cone penetrometer for Natural Gas hydrate-bearing pressure-core sediment samples recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 502-511.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Tenma, N., 2019. Consolidation and hardening behavior of hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 512-523.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Jang, J., Waite, W.F., Kumar, P., Tenma, N., 2019. Permeability variation and anisotropy of gas hydrate-

bearing pressure-core sediments recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 524-536.

Jang, J., Dai, S., Yoneda, J., Waite, W.F., Stern, L.A., Boze, L.-G., Collett, T.S., Kumar, P., 2019. Pressure core analysis of geomechanical and fluid flow properties of seals associated with gas hydrate-bearing reservoirs in the Krishna-Godavari Basin, offshore India. Marine and Petroleum Geology 108, 537-550.

Yadav, U.S., Shukla, K.M., Ojha, M., Kumar, P., Shankar, U., 2019. Assessment of gas hydrate accumulations using velocities derived from vertical seismic profiles and acoustic log data in Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 551-561.

Saumya, S., Narasimhan, B., Singh, J., Yamamoto, H., Vij, J., Sakiyama, N., Kumar, P., 2019. Acquisition of logging-while-drilling (LWD) multipole acoustic log data during the India National Gas Hydrate Program (NGHP) Expedition 02. Marine and Petroleum Geology 108, 562-569.

Jain, V., Saumya, S., Vij, J., Singh, J., Singh, B., Pattnaik, S., Oli, A., Kumar, P., Collett, T.S., 2019. New technique for accurate porosity estimation from logging-while-drilling nuclear magnetic resonance data, NGHP-02 expedition, offshore, India. Marine and Petroleum Geology 108, 570-580.

Pandey, L., Sain, K., Joshi, A.K., 2019. Estimate of gas hydrate saturations in the Krishna-Godavari basin, eastern continental margin of India, results of expedition NGHP-02. Marine and Petroleum Geology 108, 581-594.

Joshi, A.K., Sain, K., Pandey, L., 2019. Gas hydrate saturation and reservoir characterization at sites NGHP-02-17 and NGHP-02-19, Krishna Godavari Basin, eastern margin of India. Marine and Petroleum Geology 108, 595-608.

Kumar, P., Collett, T.S., Yadav, U.S., Singh, J., 2019. Formation pressure and fluid flow measurements in marine gas hydrate reservoirs, NGHP-02 expedition, offshore India. Marine and Petroleum Geology 108, 609-618.

Myshakin, E.M., Seol, Y., Lin, J.-S., Uchida, S., Collett, T.S., Boswell, R., 2019. Numerical simulations of depressurization-induced gas production from an interbedded turbidite gas hydrate-bearing sedimentary section in the offshore India: Site NGHP-02-16 (Area-B). Marine and Petroleum Geology 108, 619-638.

Uchida, S., Lin, J.-S., Myshakin, E.M., Seol, Y., Boswell, R., 2019. Numerical simulations of sand migration during gas production in hydrate-bearing sands interbedded with thin mud layers at site NGHP-02-16. Marine and Petroleum Geology 108, 639-647.

Lin, J.-S., Uchida, S., Myshakin, E.M., Seol, Y., Rutqvist, J., Boswell, R., 2019. Assessing the geomechanical stability of interbedded hydrate-bearing sediments under gas production by depressurization at NGHP-02 Site 16. Marine and Petroleum Geology 108, 648-659.

Moridis, G.J., Reagan, M.T., Queiruga, A.F., Boswell, R., 2019. Evaluation of the performance of the oceanic hydrate accumulation at site NGHP-02-09 in the Krishna-Godavari Basin during a production test and during single and multi-well production scenarios. Marine and Petroleum Geology 108, 660-696.

Kim, J., Dai, S., Jang, J., Waite, W.F., Collett, T.S., Kumar, P., 2019. Compressibility and particle crushing of Krishna-Godavari Basin sediments from offshore India: Implications for gas production from deep-water gas hydrate deposits. Marine and Petroleum Geology 108, 697-704.

Dai, S., Kim, J., Xu, Y., Waite, W.F., Jang, J., Yoneda, J., Collett, T.S., Kumar, P., 2019. Permeability anisotropy and relative permeability in sediments from the National Gas Hydrate Program Expedition 02, offshore India. Marine and Petroleum Geology 108, 705-713.

Cao, S.C., Jang, J., Jung, J., Waite, W.F., Collett, T.S., Kumar, P., 2019. 2D micromodel study of clogging behavior of fine-grained particles associated with gas hydrate production in NGHP-02 gas hydrate reservoir sediments. Marine and Petroleum Geology 108, 714-730.

Konno, Y., Kato, A., Yoneda, J., Oshima, M., Kida, M., Jin, Y., Nagao, J., Tenma, N., 2019. Numerical analysis of gas production potential from a gas-hydrate reservoir at Site NGHP-02-16, the Krishna–Godavari Basin, offshore India–Feasibility of depressurization method for ultra-deepwater environment. Marine and Petroleum Geology 108, 731-740.

Deepak, M., Kumar, P., Singh, K., Yadav, U.S., 2019. Techno-economic forecasting of a hypothetical gas hydrate field in the offshore of India. Marine and Petroleum Geology 108, 741-746.

Isotope Geochemistry


Beeler, S.R., Gomez, F.J., Bradley, A.S., 2020. Controls of extreme isotopic enrichment in modern microbialites and associated abiogenic carbonates. Geochimica et Cosmochimica Acta 269, 136-149.

Denny, A.C., Orland, I.J., Valley, J.W., 2020. Regionally correlated oxygen and carbon isotope zonation in diagenetic carbonates of the Bakken Formation. Chemical Geology 531, 119327.

He, Y., Bao, H., Liu, Y., 2020. Predicting equilibrium intramolecular isotope distribution within a large organic molecule by the cutoff calculation. Geochimica et Cosmochimica Acta 269, 292-302.

Hepp, J., Glaser, B., Juchelka, D., Mayr, C., Rozanski, K., Schäfer, I.K., Stichler, W., Tuthorn, M., Zech, R., Zech, M., 2019. Validation of a coupled δ2Hn-alkane-δ18Osugar paleohygrometer approach based on a climate chamber experiment. Biogeosciences Discussions 2019, 1-30.

Johnson, J.J., Olin, J.A., Polito, M.J., 2019. A multi-biomarker approach supports the use of compound-specific stable isotope analysis of amino acids to quantify basal carbon source use in a salt marsh consumer. Rapid Communications in Mass Spectrometry 33, 1781-1791.




Wang, P., Algeo, T.J., Zhou, Q., Yu, W., Du, Y., Qin, Y., Xu, Y., Yuan, L., Pan, W., 2019. Large accumulations of 34S-enriched pyrite in a low-sulfate marine basin: The Sturtian Nanhua Basin, South China. Precambrian Research 335, 105504.

Witkowski, C.R., Agostini, S., Harvey, B.P., van der Meer, M.T.J., Sinninghe Damsté, J.S., Schouten, S., 2019. Validation of carbon isotope fractionation in algal lipids as a pCO2 proxy using a natural CO2 seep (Shikine Island, Japan). Biogeosciences 16, 4451-4461.

CLUMPED ISOTOPES

Dong, J., Eiler, J., An, Z., Wu, N., Liu, W., Li, X., Kitchen, N., Lu, F., 2020. Clumped and stable isotopes of land snail shells on the Chinese Loess Plateau and their climatic implications. Chemical Geology 533, 119414.

Hill, P.S., Schauble, E.A., Tripati, A., 2020. Theoretical constraints on the effects of added cations on clumped, oxygen, and carbon isotope signatures of dissolved inorganic carbon species and minerals. Geochimica et Cosmochimica Acta 269, 496-539.

Kappelmann, J., Beyß, M., Nöh, K., Noack, S., 2019. Separation of 13C- and 15N-isotopologues of amino acids with a primary amine without mass resolution by means of O-phthalaldehyde derivatization and collision induced dissociation. Analytical Chemistry 91, 13407-13417.

Voglar, G.E., Zavadlav, S., Levanič, T., Ferlan, M., 2019. Measuring techniques for concentration and stable isotopologues of CO2 in a terrestrial ecosystem: A review. Earth-Science Reviews 199, 102978.

Wanner, P., Hunkeler, D., 2019. Molecular dynamic simulations of carbon and chlorine isotopologue fractionation of chlorohydrocarbons during diffusion in liquid water. Environmental Science & Technology Letters 6, 681-685.

Zhang, N., Lin, M., Yamada, K., Kano, A., Liu, Q., Yoshida, N., Matsumoto, R., 2020. The effect of H2O2 treatment on stable isotope analysis (δ13C, δ18O and Δ47) of various carbonate minerals. Chemical Geology 532, 119352.

METHODS/INSTRUMENTATION

Barrios-Guzmán, C., Sepúlveda, M., Docmac, F., Zarate, P., Reyes, H., Harrod, C., 2019. Sample acidification has a predictable effect on isotopic ratios of particulate organic matter along the Chilean coast. Rapid Communications in Mass Spectrometry 33, 1652-1659.

Becerra-Valdivia, L., Leal-Cervantes, R., Wood, R., Higham, T., 2020. Challenges in sample processing within radiocarbon dating and their impact in 14C-dates-as-data studies. Journal of Archaeological Science 113, 105043.


Van Hale, R.J., Holder, P.W., Harrison, J.D.S., Frew, R.D., 2019. Extending the limit of measurement for dual H and O isotope ratios using thermolysis. Analytical Chemistry 91, 13367-13371.

Velivetskaya, T.A., Ignatiev, A.V., Yakovenko, V.V., Vysotskiy, S.V., 2019. An improved femtosecond laser-ablation fluorination method for measurements of sulfur isotopic anomalies (∆33S and ∆36S) in sulfides with high precision. Rapid Communications in Mass Spectrometry 33, 1722-1729.


Mathematical Geochemistry/Phase Behavior

Javanmard, H., Seyyedi, M., Jones, S.A., Nielsen, S.M., 2019. Dimethyl ether enhanced oil recovery in fractured reservoirs and aspects of phase behavior. Energy & Fuels 33, 10718-10727.

Li, K., Li, H., Sun, M., Zhang, J., Zhang, H., Ren, S., Barati, M., 2019. Atomic-scale understanding about coke carbon structural evolution by experimental characterization and ReaxFF molecular dynamics. Energy & Fuels 33, 10941-10952.

Tan, S.P., Kargel, J.S., Vance, S.D., Lopes, R.M., 2019. Modeling binary mixtures of water + light hydrocarbon using the perturbed-chain statistical associating fluid theory with induced association: Improvement in describing all equilibrium phases. ACS Earth and Space Chemistry 3, 2569-2581.

Xiong, W., Bian, X.-Q., Liu, Y.-B., 2020. Phase equilibrium modeling for methane solubility in aqueous sodium chloride solutions using an association equation of state. Fluid Phase Equilibria 506, 112416.

Yang, Y., Lun, Z., Wang, R., Hu, W., 2020. Non-equilibrium phase behavior in gas condensate depletion experiments. Fluid Phase Equilibria 506, 112410.

Zhang, B., Kang, J., Kang, T., Kang, G., Zhao, G., 2019. Molecular dynamics simulations of CH4 diffusion in kaolinite: influence of water content. International Journal of Coal Science & Technology 6, 556-563.

Microbiology/Extremophiles

Atomi, H., Reeve, J., 2019. Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon. Microbiology 165, 1166-1168.

Durán-Viseras, A., Sánchez-Porro, C., Ventosa, A., 2019. Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern. International Journal of Systematic and Evolutionary Microbiology 69, 3636-3643.

Gifford, D.R., 2019. Life on the frontline reveals constraints. Nature Ecology & Evolution 3, 1501-1502.

Hallsworth, J.E., 2019. Microbial unknowns at the saline limits for life. Nature Ecology & Evolution 3, 1503-1504.

He, W., Guo, J., Guo, H., An, M., Huang, W., Wang, Y., Cai, H., 2019. Sphingobacterium puteale sp. nov., isolated from a deep subsurface aquifer. International Journal of Systematic and Evolutionary Microbiology 69, 3356-3361.

Hirano, K., Hara, T., Ardianor, Nugroho, R.A., Segah, H., Takayama, N., Sulmin, G., Komai, Y., Okada, S., Kawamura, K., 2019. Detection of the oil-producing microalga Botryococcus braunii in natural freshwater environments by targeting the hydrocarbon biosynthesis gene SSL-3. Scientific Reports 9, 16974.

Kim, J., Chhetri, G., Kim, I., Kim, H., Kim, M.K., Seo, T., 2019. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. Journal of Microbiology 57, 959-966.

Millán-Aguiñaga, N., Soldatou, S., Brozio, S., Munnoch, J.T., Howe, J., Hoskisson, P.A., Duncan, K.R., 2019. Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential. Microbiology 165, 1169-1180.

Ogwu, M.C., Srinivasan, S., Dong, K., Ramasamy, D., Waldman, B., Adams, J.M., 2019. Community ecology of Deinococcus in irradiated soil. Microbial Ecology 78, 855-872.

Spatharis, S., Lamprinou, V., Meziti, A., Kormas, K.A., Danielidis, D.D., Smeti, E., Roelke, D.L., Mancy, R., Tsirtsis, G., 2019. Everything is not everywhere: can marine compartments shape phytoplankton assemblages? Proceedings of the Royal Society B: Biological Sciences 286, 20191890.


MICROBIAL ECOSYSTEMS


Cadena, S., Aguirre-Macedo, M.L., Cerqueda-García, D., Cervantes, F.J., Herrera-Silveira, J.A., García-Maldonado, J.Q., 2019. Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico. Estuarine, Coastal and Shelf Science 230, 106433.

Chénard, C., Wijaya, W., Vaulot, D., Lopes dos Santos, A., Martin, P., Kaur, A., Lauro, F.M., 2019. Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters. Scientific Reports 9, 16390.


Donnarumma, L., Appolloni, L., Chianese, E., Bruno, R., Baldrighi, E., Guglielmo, R., Russo, G.F., Zeppilli, D., Sandulli, R., 2019. Environmental and benthic community patterns of the shallow hydrothermal area of secca Delle Fumose (Baia, Naples, Italy). Frontiers in Marine Science 6, 685. doi: 610.3389/fmars.2019.00685.


Glamoclija, M., Ramirez, S., Sirisena, K., Widanagamage, I., 2019. Subsurface microbial ecology at sediment-groundwater interface in sulfate-rich playa; White Sands National Monument, New Mexico. Frontiers in Microbiology 10, 2595. doi: 2510.3389/fmicb.2019.02595.

Hale, L., Feng, W., Yin, H., Guo, X., Zhou, X., Bracho, R., Pegoraro, E., Penton, C.R., Wu, L., Cole, J., Konstantinidis, K.T., Luo, Y., Tiedje, J.M., Schuur, E.A.G., Zhou, J., 2019. Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon. The ISME Journal 13, 2901-2915.

Harrison, J.B., Sunday, J.M., Rogers, S.M., 2019. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings of the Royal Society B: Biological Sciences 286, 20191409.

He, S., Tan, J., Hu, W., Mo, C., 2019. Diversity of archaea and its correlation with environmental factors in the Ebinur Lake wetland. Current Microbiology 76, 1417-1424.

Kadnikov, V.V., Savvichev, A.S., Mardanov, A.V., Beletsky, A.V., Merkel, A.Y., Ravin, N.V., Pimenov, N.V., 2019. Microbial communities involved in the methane cycle in the near-bottom water layer and sediments of the meromictic subarctic Lake Svetloe. Antonie van Leeuwenhoek 112, 1801-1814.

Knief, C., Bol, R., Amelung, W., Kusch, S., Frindte, K., Eckmeier, E., Jaeschke, A., Dunai, T., Fuentes, B., Mörchen, R., Schütte, T., Lücke, A., Klumpp, E., Kaiser, K., Rethemeyer, J., 2020. Tracing elevational changes in microbial life and organic carbon sources in soils of the Atacama Desert. Global and Planetary Change 184, 103078.

Lee, D.-H., Lee, Y.M., Kim, J.-H., Jin, Y.K., Paull, C., Niemann, H., Kim, J.-H., Shin, K.-H., 2019. Discriminative biogeochemical signatures of methanotrophs in different chemosynthetic habitats at an active mud volcano in the Canadian Beaufort Sea. Scientific Reports 9, 17592.


Lv, J., Liu, F., Han, W., Wang, Y., Zhu, Q., Zang, J., Wang, S., Zhang, B., Wang, N., 2019. The effect of nitrogen content on archaeal diversity in an Arctic lake region. Microorganisms 7, 10.3390/microorganisms7110543.


Rastelli, E., Corinaldesi, C., Dell’Anno, A., Tangherlini, M., Lo Martire, M., Nishizawa, M., Nomaki, H., Nunoura, T., Danovaro, R., 2019. Drivers of bacterial α- and β-diversity patterns and functioning in subsurface hadal sediments. Frontiers in Microbiology 10, 2609. doi: 2610.3389/fmicb.2019.02609.

Ruginescu, R., Purcărea, C., Dorador, C., Lavin, P., Cojoc, R., Neagu, S., Lucaci, I., Enache, M., 2019. Exploring the hydrolytic potential of cultured halophilic bacteria isolated from the Atacama Desert. FEMS Microbiology Letters 366.

Singh, R., Ryu, J., Kim, S.W., 2019. Microbial consortia including methanotrophs: some benefits of living together. Journal of Microbiology 57, 939-952.

Zhou, L., Zhou, Y., Yao, X., Cai, J., Liu, X., Tang, X., Zhang, Y., Jang, K.-S., Jeppesen, E., 2020. Decreasing diversity of rare bacterial subcommunities relates to dissolved organic matter along permafrost thawing gradients. Environment International 134, 105330.

PETROLEUM DEGRADERS



Gibu, N., Kasai, D., Ikawa, T., Akiyama, E., Fukuda, M., 2019. Characterization and transcriptional regulation of n-alkane hydroxylase gene cluster of Rhodococcus jostii RHA1. Microorganisms 7, 10.3390/microorganisms7110479








Paleoclimatology/Paleoceanography

Chen, K., Hu, D., Zhang, X., Zhu, H., Sun, L., Li, M., Shen, Y., 2020. Minor Δ33S anomalies coincide with biotic turnover events during the Great Ordovician Biodiversification Event (GOBE) in South China. Global and Planetary Change 184, 103069.

Döring, M., Leuenberger, M.C., 2019. Comparison of Holocene temperature reconstructions based on GISP2 multiple-gas-isotope measurements. Climate of the Past Discussions 2019, 1-45.

Edegbai, A.J., Schwark, L., Oboh-Ikuenobe, F.E., 2020. Nature of dispersed organic matter and paleoxygenation of the Campano-Maastrichtian dark mudstone unit, Benin flank, western Anambra Basin: Implications for Maastrichtian Trans-Saharan seaway paleoceanographic conditions. Journal of African Earth Sciences 162, 103654.

Guillemot, T., Stockhecke, M., Bechtel, A., Ladd, S.N., Nelson, D.B., Schubert, C.J., 2019. Paleoenvironmental and paleoclimatic variations around Lake Van (Eastern Turkey) recorded by sedimentary source specific biomarkers 250–130 ka (MIS7 and MIS6). Quaternary Science Reviews 225, 105997.

Kölling, M., Bouimetarhan, I., Bowles, M.W., Felis, T., Goldhammer, T., Hinrichs, K.-U., Schulz, M., Zabel, M., 2019. Consistent CO2 release by pyrite oxidation on continental shelves prior to glacial terminations. Nature Geoscience 12, 929-934.

Liebrand, D., de Bakker, A.T.M., 2019. Bispectra of climate cycles show how ice ages are fuelled. Climate of the Past 15, 1959-1983.

Percival, L.M.E., Bond, D.P.G., Rakociński, M., Marynowski, L., Hood, A.v.S., Adatte, T., Spangenberg, J.E., Föllmi, K.B., 2020. Phosphorus-cycle disturbances during the Late Devonian anoxic events. Global and Planetary Change 184, 103070.


Vellekoop, J., Woelders, L., Sluijs, A., Miller, K.G., Speijer, R.P., 2019. Phytoplankton community disruption caused by latest Cretaceous global warming. Biogeosciences 16, 4201-4210.

Vickers, M.L., Price, G.D., Jerrett, R.M., Sutton, P., Watkinson, M.P., FitzPatrick, M., 2019. The duration and magnitude of Cretaceous cool events: Evidence from the northern high latitudes. GSA Bulletin 131, 1979-1994.

Yao, W., Paytan, A., Wortmann, U.G., 2020. Effects of a transient marine sulfur reservoir on seawater δ18OSO4 during the Paleocene-Eocene Thermal Maximum. Geochimica et Cosmochimica Acta 269, 257-269.

Zhang, B., Yao, S., Mills, B.J.W., Wignall, P.B., Hu, W., Liu, B., Ren, Y., Li, L., Shi, G., 2020. Middle Permian organic carbon isotope stratigraphy and the origin of the Kamura Event. Gondwana Research 79, 217-232.

EXTINCTION EVENTS

Elewa, A.M.T., Abdelhady, A.A., 2020. Past, present, and future mass extinctions. Journal of African Earth Sciences 162, 103678.

Henehan, M.J., Ridgwell, A., Thomas, E., Zhang, S., Alegret, L., Schmidt, D.N., Rae, J.W.B., Witts, J.D., Landman, N.H., Greene, S.E., Huber, B.T., Super, J.R., Planavsky, N.J., Hull, P.M., 2019. Rapid ocean acidification and protracted Earth system recovery followed the end-Cretaceous Chicxulub impact. Proceedings of the National Academy of Sciences 116, 22500-22504.

Karabeyoğlu, A.U., Özkan-Altıner, S., Altıner, D., 2019. Quantitative analysis of planktonic foraminifera across the Cretaceous-Paleogene transition and observations on the extinction horizon, Haymana Basin, Turkey. Cretaceous Research 104, 104169.

Liao, Z., Hu, W., Cao, J., Wang, X., Fu, X., 2020. Oceanic anoxia through the late Permian Changhsingian Stage in the Lower Yangtze region, South China: Evidence from sulfur isotopes and trace elements. Chemical Geology 532, 119371.

Lin, J.-P., Sundberg, F.A., Jiang, G., Montañez, I.P., Wotte, T., 2019. Chemostratigraphic correlations across the first major trilobite extinction and faunal turnovers between Laurentia and South China. Scientific Reports 9, 17392.

Lyson, T.R., Miller, I.M., Bercovici, A.D., Weissenburger, K., Fuentes, A.J., Clyde, W.C., Hagadorn, J.W., Butrim, M.J., Johnson, K.R., Fleming, R.F., Barclay, R.S., Maccracken, S.A., Lloyd, B., Wilson, G.P., Krause, D.W., Chester, S.G.B., 2019. Exceptional continental record of biotic recovery after the Cretaceous–Paleogene mass extinction. Science 366, 977.

Smits, P., Finnegan, S., 2019. How predictable is extinction? Forecasting species survival at million-year timescales. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190392.

Wei, H., Tang, Z., Yan, D., Wang, J., Roberts, A.P., 2019. Guadalupian (Middle Permian) ocean redox evolution in South China and its implications for mass extinction. Chemical Geology 530, 119318.

Wu, K., Tian, L., Liang, L., Metcalfe, I., Chu, D., Tong, J., 2019. Recurrent biotic rebounds during the Early Triassic: biostratigraphy and temporal size variation of conodonts from the Nanpanjiang Basin, South China. Journal of the Geological Society 176, 1232.

Petroleum Systems

EXPLORATION

Burwicz, E., Haeckel, M., 2020. Basin-scale estimates on petroleum components generation in the Western Black Sea basin based on 3-D numerical modelling. Marine and Petroleum Geology 113, 104122.


Deng, Y., 2019. Control effect of the gulf on marine petroleum. Petroleum Research 4, 283-294.

El Ghamry, M.N., El Amawy, M., Hagag, W., 2020. The role of Late Cretaceous wrench tectonics in hydrocarbon endowment in El-Gindi Basin, northern Western Desert, Egypt. Marine and Petroleum Geology 112, 104093.

Huang, C., Liu, G., Ma, Y., Zhou, X., Zhang, L., Yin, J., Guo, J., 2019. Hydrocarbon migration in fracture-cave systems of carbonate reservoirs under tectonic stresses: A modeling study. Petroleum Research 4, 354-364.


Ma, X., Huang, C., Shi, Y., 2019. Oil and gas enrichment patterns and major controlling factors for stable and high production of tight lacustrine carbonate rocks, a case study of Yingxi area in Qaidam Basin, West China. Carbonates and Evaporites 34, 1815-1831.

Mukhopadhyay, D.K., 2019. Petroleum system in Indian Collision Zone: Perspective from structural geology. Journal of the Geological Society of India 94, 549-549.

Shorten, C.M., Fitzgerald, P.G., 2019. Post-orogenic thermal history and exhumation of the northern Appalachian Basin: Low-temperature thermochronologic constraints. Basin Research 31, 1017-1039.

Vatandoust, M., Faghih, A., Asadi, S., Azimzadeh, A.M., Heidarifard, M.H., 2020. Study of hydrocarbon generation and 1D-2D modeling of hydrocarbon migration at the Karanj and Parsi oilfields, Southern Dezful Embayment, SW Iran. Marine and Petroleum Geology 113, 104095.

Wang, C., Zeng, J., Zhang, Z., Yu, Y., Wang, F., Liu, X., 2019. Geological characteristics and hydrocarbon potential of the detachment basin in the Baiyun depression, Pearl River Mouth Basin, South China Sea. Energy & Fuels 33, 10519-10532.


Yang, H., Li, Y., Tang, Y., Lei, G., Sun, X., Zhou, P., Zhou, L., Xu, A., Tang, J., Zhu, W., Shang, J., Chen, W., Li, M., 2019. Reservoir accumulation conditions and key exploration & development technologies for Keshen gas field in Tarim Basin. Petroleum Research 4, 295-313.

Zhang, M.-h., Qiao, J.-h., Zhao, G.-x., Lan, X.-y., 2019. Regional gravity survey and application in oil and gas exploration in China. China Geology 2, 382-390.

GENERATION & EXPULSION

Ma, X., Huang, C., Shi, Y., Chang, H., Zhao, F., 2019. Unique hydrocarbon-generating mechanism of Oligocene evaporites of Qaidam Basin, West China. Carbonates and Evaporites 34, 1455-1467.

Misra, S., Das, S.K., Varma, A.K., Mani, D., Kalpana, M.S., Ekblad, A., Biswas, S., 2020. Multi-proxy approach on the hydrocarbon generation perspective of Barjora Basin, India. Marine and Petroleum Geology 112, 104108.

Pan, N., Li, D., Lü, W., Dai, F., 2019. Kinetic study on the pyrolysis behavior of Jimsar oil shale Oil Shale 36, 462–482.

Pan, S., Wang, Q., Bai, J., Liu, H., Chi, M., Cui, D., Xu, F., 2019. Investigation of behavior of sulfur in oil fractions during oil shale pyrolysis. Energy & Fuels 33, 10622-10637.


Shao, D., Zhang, T., Ko, L.T., Li, Y., Yan, J., Zhang, L., Luo, H., Qiao, B., 2020. Experimental investigation of oil generation, retention, and expulsion within Type II kerogen-dominated marine shales: Insights from gold-tube nonhydrous pyrolysis of

Barnett and Woodford Shales using miniature core plugs. International Journal of Coal Geology 217, 103337.

OIL & GAS

Abu-Mahfouz, I.S., Cartwright, J.A., Idiz, E., Hooker, J.N., Robinson, S., van den Boorn, S., 2019. Genesis and role of bitumen in fracture development during early catagenesis. Petroleum Geoscience 25, 371.

Alipour, M., Alizadeh, B., Chehrazi, A., Mirzaie, S., 2019. Combining biodegradation in 2D petroleum system models: application to the Cretaceous petroleum system of the southern Persian Gulf basin. Journal of Petroleum Exploration and Production Technology 9, 2477-2486.

Gan, H., Wang, H., Shi, Y., Ma, Q., Liu, E., Yan, D., Pan, Z., 2020. Geochemical characteristics and genetic origin of crude oil in the Fushan sag, Beibuwan Basin, South China Sea. Marine and Petroleum Geology 112, 104114.

Gong, D., Zhang, Y., Guo, W., Qi, R., Lu, S., Wu, W, 2019. Identification of secondary microbial methane and biodegradation: Case study from Luliang oil and gas field, Junggar Basin, China. Journal of Natural Gas Geoscience 4, 267-278.

Li, Y., Chen, S., Lu, J., Wang, G., Zou, X., Xiao, Z., Su, K., He, Q., Luo, X., 2020. The logging recognition of solid bitumen and its effect on physical properties, AC, resistivity and NMR parameters. Marine and Petroleum Geology 112, 104070.


Song, Y., Wang, X., Guo, X., Liu, C., Li, H., Liu, D., 2020. Analysis on causes of differences in physical properties of Jurassic crude oil around Fukang depression, Junggar Basin. Petroleum Science and Technology 38, 75-82.

Thompson-Butler, W., Peters, K.E., Magoon, L.B., Scheirer, A.H., Moldowan, J.M., Blanco, V.O., Gonzalez, R.E., Graham, S.A., Zumberge, J.E., Wavrek, D.A., 2019. Identification of genetically distinct petroleum tribes in the Middle Magdalena Valley, Colombia. American Association of Petroleum Geologists Bulletin 103, 3003-3034.

Wang, N., Li, M., Liu, X., Hong, H., Tian, X., Yang, C., Shi, S., Liu, P., 2020. Geo-chromatographic fractionation effect of methyldibenzofuran in dolomite reservoirs and its application in tracing oil filling pathways in the Sichuan Basin. Marine and Petroleum Geology 113, 104126.

Wei, Y., Chen, G., Lu, S., Song, Z., Qi, R., Wang, W., Gong, D., Wang, F., 2019. Re-examination of genetic types and origins of natural gases from Dibei bulge, eastern Luliang uplift, Junggar Basin, China. Journal of Natural Gas Geoscience 4, 257-265.


SOURCE ROCKS


Alnahwi, A., Loucks, R.G., 2019. Mineralogical composition and total organic carbon quantification using x-ray fluorescence data from the Upper Cretaceous Eagle Ford Group in southern Texas. American Association of Petroleum Geologists Bulletin 103, 2891-2907.

Atar, E., März, C., Schnetger, B., Wagner, T., Aplin, A., 2019. Local to global controls on the deposition of organic-rich muds across the Late Jurassic Laurasian Seaway. Journal of the Geological Society 176, 1143.

Baioumy, H., Lehmann, B., Ahmed Salim, A.M., Al-Kahtany, K., El-Sorogy, A., 2020. Geochemical characteristics of black shales from Triassic turbidites, Peninsular Malaysia: Implications for their origin and tectonic setting. Marine and Petroleum Geology 113, 104137.


Chen, Z., Zhang, C., 2019. The characteristics and hydrocarbon-generation model of Paleogene–Neogene System saline lacustrine facies source rocks in the Western Qaidam Basin, China. Journal of Petroleum Exploration and Production Technology 9, 2441-2447.

Cichon-Pupienis, A., Littke, R., Froidl, F., Lazauskienė, J., 2020. Depositional history, source rock quality and thermal maturity of Upper Ordovician - Lower Silurian organic-rich sedimentary rocks in the central part of the Baltic Basin (Lithuania). Marine and Petroleum Geology 112, 104083.

Cruz Luque, M., Aguilera, R., 2019. Eagle Ford and Pimienta shales in Mexico: A case study. SPE-191644-PA 22, 1305-1322.

Deaf, A.S., Tahoun, S.S., Gentzis, T., Carvajal-Ortiz, H., Harding, I.C., Marshall, J.E.A., Ocubalidet, S., 2020. Organic geochemical, palynofacies, and petrographic analyses examining the hydrocarbon potential of the Kharita Formation (Albian) in the Matruh Basin, northwestern Egypt. Marine and Petroleum Geology 112, 104087.

Gordadze, G.N., Giruts, M.V., Poshibaeva, A.R., Poshibaev, V.V., Gayanova, A.A., Postnikov, A.V., Postnikova, O.V., 2019. Study of the structure of benzene- and alcohol–benzene-extractable resins and kerogen of rock organic matter (by example of Bazhenovo Formation rocks from the north of the Gyda Peninsula). Petroleum Chemistry 59, 1177-1189.



Hallek, T., Akrout, D., Ahmadi, R., Montacer, M., 2020. Assessment of sedimentary environment from PAHs and aliphatic biomarkers: The case study of Fahdene black shales in northern Tunisia. Journal of African Earth Sciences 161, 103676.

Jagadisan, A., Heidari, Z., 2019. Experimental quantification of the effect of thermal maturity of kerogen on its wettability. SPE-191644-PA 22, 1323-1333.

Kong, X., Jiang, Z., Han, C., Zhang, R., 2020. Organic matter enrichment and hydrocarbon accumulation models of the marlstone in the Shulu Sag, Bohai Bay Basin, Northern China. International Journal of Coal Geology 217, 103350.

Li, J., Wang, M., Chen, Z., Lu, S., Jiang, C., Chen, G., Tian, S., 2019. Evaluating the total oil yield using a single routine Rock-Eval experiment on as-received shales. Journal of Analytical and Applied Pyrolysis 144, 104707.

Liu, B., Mastalerz, M., Schieber, J., Teng, J., 2020. Association of uranium with macerals in marine black shales: Insights from the Upper Devonian New Albany Shale, Illinois Basin. International Journal of Coal Geology 217, 103351.

Luo, Q., Fariborz, G., Zhong, N., Wang, Y., Qiu, N., Skovsted, C.B., Suchý, V., Hemmingsen Schovsbo, N., Morga, R., Xu, Y., Hao, J., Liu, A., Wu, J., Cao, W., Min, X., Wu, J., 2020. Graptolites as fossil geo-thermometers and source material of hydrocarbons: An overview of four decades of progress. Earth-Science Reviews 200, 103000.


Müller, S., Arfai, J., Jähne-Klingberg, F., Bense, F., Weniger, P., 2020. Source rocks of the German Central Graben. Marine and Petroleum Geology 113, 104120.

Nazir, A., Iqbal, M., Siddique, A., Ahmed, W., 2020. Evaluation of source, depositional environment, thermal maturity and biodegradation of organic matter from Kohat-Potwar Basin, Pakistan. Petroleum Science and Technology 38, 106-115.

Paul, S., Gross, D., Bechtel, A., Dutta, S., 2020. Preservation of monoterpenoids in Oligocene resin: Insights into the evolution of chemical defense mechanism of plants in deep-time. International Journal of Coal Geology 217, 103326.


Philp, R.P., DeGarmo, C.D., 2020. Geochemical characterization of the Devonian-Mississippian Woodford Shale from the McAlister Cemetery Quarry, Criner Hills Uplift, Ardmore Basin, Oklahoma. Marine and Petroleum Geology 112, 104078.


Roberts, J., Heij, G., Elmore, R.D., 2019. Palaeomagnetic dating of hydrothermal alteration in the Woodford Shale, Oklahoma, USA. Geological Magazine 156, 2043-2052.

Sadooni, F.N., Alsharhan, A.S., 2019. Regional stratigraphy, facies distribution, and hydrocarbons potential of the Oligocene strata across the Arabian Plate and Western Iran. Carbonates and Evaporites 34, 1757-1770.

Song, Y., Hu, S., Xu, J., Shen, C., Li, S., Su, P., Xie, W., 2020. Lacustrine environmental evolution and implications on source rock deposition in the Upper Cretaceous-Paleocene of the South Yellow Sea Basin, offshore eastern China. Marine and Petroleum Geology 113, 104135.

Sun, L., Yin, C., Liu, C., Zeng, H., Zhang, Y., Xu, Y., Cai, D., 2019. Geological characteristics and exploration significance of high-quality source rocks in Yingcheng Formation, Songliao Basin. Acta Petrolei Sinica 40, 1172-1179.

Zhang, J., Cao, J., Xiang, B., Zhou, N., Ma, W., Li, E., 2019. Fourier-transform infrared proxies for oil source and maturity: Insights from the early Permian alkaline lacustrine system, Junggar Basin (NW China). Energy & Fuels 33, 10704-10717.

Zhang, M., Li, Z., 2019. Biodegradation characteristics of oil shale in the Permian Lucaogou Formation in the southeast of the Junggar Basin, China: implications from organic geochemistry. Oil Shale 36, 501–513.

Zhang, Q., Littke, R., Zieger, L., Shabani, M., Tang, X., Zhang, J., 2019. Ediacaran, Cambrian, Ordovician, Silurian and Permian shales of the Upper Yangtze Platform, South China: Deposition, thermal maturity and shale gas potential. International Journal of Coal Geology 216, 103281.

UNCONVENTIONALS



Fang, C., Yang, Y., Sun, S., Qiao, R., 2020. Low salinity effect on the recovery of oil trapped by nanopores: A molecular dynamics study. Fuel 261, 116443.

Fang, Y., Yang, E., Cui, X., 2019. Study on distribution characteristics and displacement mechanism of microscopic residual oil in heterogeneous low permeability reservoirs. Geofluids 2019, 9752623.

Feng, R., Chen, S., Pang, Y., 2019. Simultaneous determination of permeability and diffusivity subject to dynamic sorption in gas shales. International Journal of Coal Geology 216, 103294.

Hazra, B., Chandra, D., Singh, A.K., Varma, A.K., Mani, D., Singh, P.K., Boral, P., Buragohain, J., 2019. Comparative pore structural attributes and fractal dimensions of Lower Permian organic-matter-bearing sediments of two Indian basins: Inferences from nitrogen gas adsorption. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 2975-2988.

He, L., Mei, H., Hu, X., Dejam, M., Kou, Z., Zhang, M., 2019. Advanced flowing material balance to determine original gas in place of shale gas considering adsorption hysteresis. SPE-191644-PA 22, 1282-1292.

Huang, H., Li, R., Jiang, Z., Li, J., Chen, L., 2020. Investigation of variation in shale gas adsorption capacity with burial depth: Insights from the adsorption potential theory. Journal of Natural Gas Science and Engineering 73, 103043.

Inan, M.A., Kavak, O., 2019. Shale resource potential of the Silurian Dadas Formation in Diyarbakır (SE Anatolia of Turkey) and its surroundings. Arabian Journal of Geosciences 12, 679.


Jiang, Y., Liu, X., Fu, Y., Chen, H., Zhang, H., Yan, J., Chen, C., Gu, Y., 2019. Evaluation of effective porosity in marine shale reservoir, western Chongqing Acta Petrolei Sinica 40, 1233-1243

Jimenez, B.A.L., Aguilera, R., 2019. Physics-based fluid-flow modeling of liquids-rich shale reservoirs using a 3D three-phase multiporosity numerical-simulation model. SPE-191644-PA 22, 1501-1526.

Klewiah, I., Berawala, D.S., Alexander Walker, H.C., Andersen, P.Ø., Nadeau, P.H., 2020. Review of experimental sorption studies of CO2 and CH4 in shales. Journal of Natural Gas Science and Engineering 73, 103045.

Li, J., Wang, M., Lu, S., Chen, G., Tian, W., Jiang, C., Li, Z., 2020. A new method for predicting sweet spots of shale oil using conventional well logs. Marine and Petroleum Geology 113, 104097.

Li, M., Chen, Z., Qian, M., Ma, X., Jiang, Q., Li, Z., Tao, G., Wu, S., 2020. What are in pyrolysis S1 peak and what are missed? Petroleum compositional characteristics revealed

from programed pyrolysis and implications for shale oil mobility and resource potential. International Journal of Coal Geology 217, 103321.

Li, Z., Qiu, N., Liu, N., Cai, C., Tian, J., Wang, Y., Gao, T., Gu, Q., 2019. Applying quantitative fluorescence techniques to characterize mechanism of hydrocarbon migration and accumulation in thick source strata: a case study of Member 4 of Shahejie Formation, Langgu sag in Bohai Bay Basin Acta Petrolei Sinica 40, 1158-1171.

Liu, J., Hu, Y., Kang, Y., Chen, H., Liu, Y., Liu, F., Liu, Z., 2019. Experimental study on fracture propagation induced by supercritical CO2 jet fracturing in artificial samples with prefabricated bedding planes. Journal of Natural Gas Science and Engineering 72, 103037.

Liu, Z., Chen, D., Zhang, J., Lv, X., Dang, W., Liu, Y., Liao, W., Li, J., Wang, Z., Wang, F., 2019. Combining isotopic geochemical data and logging data to predict the range of the total gas content in shale: A case study from the Wufeng and Longmaxi shales in the Middle Yangtze area, South China. Energy & Fuels 33, 10487-10498.

Liu, Z., Zhang, F., Li, X., 2019. Elastic anisotropy and its influencing factors in organic-rich marine shale of southern China. Science China Earth Sciences 62, 1805-1818.



Meng, X., Xie, R., Jia, H., Li, H., 2019. Identification of light oil in 2D NMR spectra of tight sandstone reservoirs by using L1/L2 two-parameter regularization. Energy & Fuels 33, 10537-10546.



Peng, S., Ren, B., Meng, M., 2019. Quantifying the influence of fractures for more-accurate laboratory measurement of shale matrix permeability using a modified gas-expansion method. SPE-191644-PA 22, 1293-1304.

Piedrahita, J., Aguilera, R., 2019. Geochemical Productivity Index (Igp): An innovative way to identify potential zones with moveable oil in shale reservoirs. SPE-191644-PA 22, 1256-1264.

Shang, Z., Dong, L., Niu, L., Shi, H., 2019. Adsorption of methane, nitrogen, and carbon dioxide in atomic-scale fractal nanopores by Monte Carlo simulation I: Single-component adsorption. Energy & Fuels 33, 10457-10475.

Shen, C., Zhao, J., Ren, L., Fan, Y., 2019. A new fracturing sweet spot identification method in Longmaxi Formation of Sichuan Basin, SW China. Journal of Natural Gas Geoscience 4, 279-286.



Verma, A., Chauhan, G., Ojha, K., Padmanabhan, E., 2019. Characterization of nano-Fe2O3-stabilized polymer-free foam fracturing fluids for unconventional gas reservoirs. Energy & Fuels 33, 10570-10582.

Wang, X., Liu, L., Wang, Y., Sheng, Y., Zheng, S., Luo, Z., 2019. Control of lithofacies on pore space of shale from Longmaxi Formation, southern Sichuan Basin. Acta Petrolei Sinica 40, 1192-1201

Wang, Y.-f., Zhai, G.-y., Lu, Y.-c., Ma, Y.-q., Li, J., Liu, G.-h., Zhang, Y.-x., 2019. Sedimentary lithofacies characteristics and sweet-spot interval characterization of the Sinian Doushantuo Formation in Upper Yangtze Platform, South China. China Geology 2, 261-275.

Wang, Y., Zhu, Y., Zhang, R., Anovitz, L.M., Bleuel, M., Liu, S., Chen, S., 2020. SANS coupled with fluid invasion approaches for characterization of overall nanopore structure and mesopore connectivity of organic-rich marine shales in China. International Journal of Coal Geology 217, 103343.

Xu, H., 2020. Probing nanopore structure and confined fluid behavior in shale matrix: A review on small-angle neutron scattering studies. International Journal of Coal Geology 217, 103325.

Zeng, F., Peng, F., Guo, J., Rui, Z., Xiang, J., 2019. Gas mass transport model for microfractures considering the dynamic variation of width in shale reservoirs. SPE-191644-PA 22, 1265-1281.


Zhao, X., Pu, X., Zhou, L., Jin, F., Shi, Z., Han, W., Jiang, W., Zhang, W., 2020. Typical geological characteristics and exploration practices of lacustrine shale oil: A case study of the Kong-2 member strata of the Cangdong Sag in the Bohai Bay Basin. Marine and Petroleum Geology 113, 103999.

Zhu, F., Hu, W., Cao, J., Ferrante, G., Pasin, M., Zhou, B., Korb, J.-P., 2019. Probing dynamics and wettability of water and oil in conventional and unconventional sandstone rock cores by field-cycling NMR relaxometry. Energy & Fuels 33, 10583-10592.

Precambrian Geochemistry

Killingsworth, B.A., Sansjofre, P., Philippot, P., Cartigny, P., Thomazo, C., Lalonde, S.V., 2019. Constraining the rise of oxygen with oxygen isotopes. Nature Communications 10, 4924.

Marty, B., Bekaert, D.V., Broadley, M.W., Jaupart, C., 2019. Geochemical evidence for high volatile fluxes from the mantle at the end of the Archaean. Nature 575, 485-488.

Warr, O., Giunta, T., Ballentine, C.J., Sherwood Lollar, B., 2019. Mechanisms and rates of 4He, 40Ar, and H2 production and accumulation in fracture fluids in Precambrian Shield environments. Chemical Geology 530, 119322.

ORGANICS/MICROFOSSILS/MICROBIAL EVOLUTION

Ai, J.Y., George, S.C., Zhong, N.N., 2020. Organic geochemical characteristics of highly mature Late Neoproterozoic black shales from South China: Reappraisal of syngeneity and indigeneity of hydrocarbon biomarkers. Precambrian Research 336, 105508.

Alleon, J., Flannery, D.T., Ferralis, N., Williford, K.H., Zhang, Y., Schuessler, J.A., Summons, R.E., 2019. Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments. Scientific Reports 9, 16712.

Burzynski, G., Dececchi, T.A., Narbonne, G.M., Dalrymple, R.W., 2020. Cryogenian Aspidella from northwestern Canada. Precambrian Research 336, 105507.


Dodd, M.S., Papineau, D., Pirajno, F., Wan, Y., Karhu, J.A., 2019. Minimal biomass deposition in banded iron formations inferred from organic matter and clay relationships. Nature Communications 10, 5022.

Jones, S.M., Prave, A.R., Raub, T.D., Cloutier, J., Stüeken, E.E., Rose, C.V., Linnekogel, S., Nazarov, K., 2020. A marine origin for the late Mesoproterozoic Copper Harbor and Nonesuch Formations of the Midcontinent Rift of Laurentia. Precambrian Research 336, 105510.

Kuang, H.-w., Fan, Z.-x., Liu, Y.-q., Peng, N., Zhu, Z.-c., Yang, Z.-r., Wang, Z.-x., Yu, H.-l., Zhong, Q., 2019. Stromatolite characteristics of Mesoproterozoic Shennongjia Group in the northern margin of Yangtze Block, China. China Geology 2, 364-381.

McMahon, S., 2019. Earth's earliest and deepest purported fossils may be iron-mineralized chemical gardens. Proceedings of the Royal Society B: Biological Sciences 286, 20192410.


PALEOCLIMATOLOGY/PALEOCEANOGRAPHY

Ostrander, C.M., Kendall, B., Olson, S.L., Lyons, T.W., Gordon, G.W., Romaniello, S.J., Zheng, W., Reinhard, C.T., Roy, M., Anbar, A.D., 2020. An expanded shale δ98Mo record permits recurrent shallow marine oxygenation during the Neoarchean. Chemical Geology 532, 119391.

Paula-Santos, G.M., Caetano-Filho, S., Enzweiler, J., Navarro, M.S., Babinski, M., Guacaneme, C., Kuchenbecker, M., Reis, H., Trindade, R.I.F., 2020. Rare earth elements in the terminal Ediacaran Bambuí Group carbonate rocks (Brazil): evidence for high seawater alkalinity during rise of early animals. Precambrian Research 336, 105506.

Wang, R., Shen, B., 2019. Snowball Earth at low solar luminosity prevented by the ocean–atmosphere coupling. Acta Geochimica 38, 775-784.

CRUSTAL EVOLUTION

Carlson, R.W., Garçon, M., O’Neil, J., Reimink, J., Rizo, H., 2019. The nature of Earth’s first crust. Chemical Geology 530, 119321.

Kumari, S., Paul, D., Stracke, A., 2019. Constraints on Archean crust formation from open system models of Earth evolution. Chemical Geology 530, 119307.

Santosh, M., Tsunogae, T., Yang, C.-X., Han, Y.-S., Hari, K.R., Prasanth, M.P.M., Uthup, S., 2020. The Bastar craton, central India: A window to Archean – Paleoproterozoic crustal evolution. Gondwana Research 79, 157-184.

Production/Engineering Geochemistry

Cui, Q., Ma, X., Nakabayashi, K., Nakano, K., Miyawaki, J., Al-Mutairi, A., Marafi, A.M.J., Al-Otaibi, A.M., Yoon, S.-H., Mochida, I., 2019. Changes in composition and molecular structures of atmospheric residues during hydrotreating. Energy & Fuels 33, 10787-10794.

Gizatullin, B., Gafurov, M., Vakhin, A., Rodionov, A., Mamin, G., Orlinskii, S., Mattea, C., Stapf, S., 2019. Native vanadyl complexes in crude oil as polarizing agents for in situ proton dynamic nuclear polarization. Energy & Fuels 33, 10923-10932.

Grimmer, C., Rüger, C.P., Streibel, T., Cuoq, F., Kwakkenbos, G., Cordova, M., Peñalver, R., Zimmermann, R., 2019. Description of steam cracker fouling and coking residues by thermal analysis-photoionization mass spectrometry. Energy & Fuels 33, 11592-11602.



Mishin, A.S., Dubinich, V.N., Svarovskaya, N.A., Dadashev, M.N., Khlebnikov, V.N., 2019. Features of the methods for the production of viscous oil from oil rims of the Cenomanian horizon. Chemistry and Technology of Fuels and Oils 55, 424-431.

Zhang, Y., Huang, S., Sheng, J.J., Jiang, Q., 2020. Experimental and analytical study of oxygen consumption during air injection in shale oil reservoirs. Fuel 262, 116462.

ASPHALTENES

Bassir, S.M., Madani, M., 2019. Predicting asphaltene precipitation during titration of diluted crude oil with paraffin using artificial neural network (ANN). Petroleum Science and Technology 37, 2397-2403.

Casas, Y.A., Duran, J.A., Schoeggl, F.F., Yarranton, H.W., 2019. Settling of asphaltene aggregates in n-alkane diluted bitumen. Energy & Fuels 33, 10687-10703.

Golsefatan, A., Shahbazi, K., 2020. Predicting the effect of nanocomposites on asphaltene removal using a comprehensive approach. Petroleum Science and Technology 38, 64-73.

Kayukova, G.P., Mikhailova, A.N., Vandyukova, I.I., 2020. Features of the elemental, structural-group, and microelement composition of asphaltenes from natural bitumens of the Permian deposits of Tatarstan. Petroleum Science and Technology 38, 18-23.

Kradra Brahma, K., Bendedouch, D., Bouhadda, Y., Bouanani, F., Bounaceur, B., Sardi, A., 2019. Stability of Hassi-Messaoud asphaltenes in media of different polarities. Petroleum Chemistry 59, 1190-1194.

Larichev, Y.V., Kovalenko, E.Y., Mart’yanov, O.N., 2019. Effect of nitrogen bases on the structure of primary asphaltene clusters and dynamics of aggregation of heavy oil fractions. Petroleum Chemistry 59, 1195-1200.

Ok, S., Mal, T.K., 2019. NMR spectroscopy analysis of asphaltenes. Energy & Fuels 33, 10391-10414.

Sepideh, K., Lotfollahi, M.N., Shahrabadi, A., 2019. Asphaltene adsorption using nanoparticles with different surface chemistry: Equilibrium and thermodynamics studies. Petroleum Chemistry 59, 1201-1206.

Shui, H., Zhao, L., Sun, J., Shui, T., Pan, C., Wang, Z., Lei, Z., Ren, S., Kang, S., Xu, C.C., 2020. Hydro-liquefaction of asphaltene from a lignite for potential jet fuel. Fuel 262, 116435.

Wei, J., Li, J., Zhou, X., Zhang, X., 2020. Effect of pressure and CO2 content on the asphaltene precipitation in the light crude oil. Petroleum Science and Technology 38, 116-123.

INTERFACES/EOR


Al-Mudhafar, W.J., 2019. Polynomial and nonparametric regressions for efficient predictive proxy metamodeling: Application through the CO2-EOR in shale oil reservoirs. Journal of Natural Gas Science and Engineering 72, 103038.

Al Maskari, N.S., Saeedi, A., Xie, Q., 2019. Alcohol-assisted waterflooding in carbonate reservoirs. Energy & Fuels 33, 10651-10658.


Amrouche, F., Gomari, S.R., Islam, M., Donglai, X., 2019. New insights into the application of a magnetic field to enhance oil recovery from oil-wet carbonate reservoirs. Energy & Fuels 33, 10602-10610.

Belhaj, A.F., Elraies, K.A., Janjuhah, H.T., Tasfy, S.F.H., Yahya, N., Abdullah, B., Umar, A.A., Ghanem, O.B., Alnarabiji, M.S., 2019. Electromagnetic waves-induced hydrophobic multiwalled carbon nanotubes for enhanced oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2667-2670.

Dang, C., Nghiem, L., Fedutenko, E., Gorucu, S.E., Yang, C., Mirzabozorg, A., Nguyen, N., Chen, Z., 2020. AI based mechanistic modeling and probabilistic forecasting of hybrid low salinity chemical flooding. Fuel 261, 116445.

Darvish Sarvestani, A., Ayatollahi, S., Bahari Moghaddam, M., 2019. Smart water flooding performance in carbonate reservoirs: an experimental approach for tertiary oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2643-2657.




Gao, H., Zhang, B., Fan, L., Zhang, H., Chen, G., Tontiwachwuthikul, P., Liang, Z., 2019. Study on diffusivity of CO2 in oil-saturated porous media under high pressure and temperature. Energy & Fuels 33, 11364-11372.

Gizzatov, A., Mashat, A., Kosynkin, D., Alhazza, N., Kmetz, A., Eichmann, S.L., Abdel-Fattah, A.I., 2019. Nanofluid of petroleum sulfonate nanocapsules for enhanced oil recovery in high-temperature and high-salinity reservoirs. Energy & Fuels 33, 11567-11573.


Iwase, M., Liang, Y., Masuda, Y., Morimoto, M., Matsuoka, T., Boek, E.S., Kaito, Y., Nakagawa, K., 2019. Application of a digital oil model to solvent-based enhanced oil recovery of heavy crude oil. Energy & Fuels 33, 10868-10877.




Soltani, P., Sadeghnejad, S., Saeedi Dehaghani, A.H., Ashena, R., 2019. Quantitative monitoring of cleaning time and wettability alteration of carbonate rocks during soxhlet cleaning. SPE-191644-PA 22, 1334-1345.

Thorne, R.J., Sundseth, K., Bouman, E., Czarnowska, L., Mathisen, A., Skagestad, R., Stanek, W., Pacyna, J.M., Pacyna, E.G., 2020. Technical and environmental viability of a European CO2 EOR system. International Journal of Greenhouse Gas Control 92, 102857.

Xiao, P., Lv, C., Wang, R., Cui, M., Xu, Q., Hu, Q., Hu, W., 2019. Laboratory study heterogeneity impact on microscopic residual oil distribution in tight sandstone cores during CO2 immiscible flooding. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 2895-2905.

Yazdani Sadati, E., Sahraei, E., 2019. An experimental investigation on enhancing water flooding performance using oil-in-water emulsions in an Iranian oil reservoir. Journal of Petroleum Exploration and Production Technology 9, 2613-2624.

Recent Sediments

Arellano, A.R., Bianchi, T.S., Osburn, C.L., D'Sa, E.J., Ward, N.D., Oviedo-Vargas, D., Joshi, I.D., Ko, D.S., Shields, M.R., Kurian, G., Green, J., 2019. Mechanisms of organic matter

export in estuaries with contrasting carbon sources. Journal of Geophysical Research: Biogeosciences 124, 3168-3188.

Arnold, T.E., Brenner, M., Kenney, W.F., Bianchi, T.S., 2019. Recent trophic state changes of selected Florida lakes inferred from bulk sediment geochemical variables and biomarkers. Journal of Paleolimnology 62, 409-423.

Cañavate, J.-P., van Bergeijk, S., Giráldez, I., González-Ortegón, E., Vílas, C., 2019. Fatty acids to quantify phytoplankton functional groups and their spatiotemporal dynamics in a highly turbid estuary. Estuaries and Coasts 42, 1971-1990.

Cappelli, E.L.G., Clarke, J.L., Smeaton, C., Davidson, K., Austin, W.E.N., 2019. Organic-carbon-rich sediments: benthic foraminifera as bio-indicators of depositional environments. Biogeosciences 16, 4183-4199.

Fernandes, D., Wu, Y., Shirodkar, P.V., Pradhan, U.K., Zhang, J., Limbu, S.M., 2020. Sources and preservation dynamics of organic matter in surface sediments of Narmada River, India – Illustrated by amino acids. Journal of Marine Systems 201, 103239.


Kaiser, J., Wasmund, N., Kahru, M., Wittenborn, A.K., Hansen, R., Häusler, K., Moros, M., Schulz-Bull, D., Arz, H.W., 2019. Reconstructing N2-fixing cyanobacterial blooms in the Baltic Sea beyond observations using 6- and 7-methylheptadecanes in sediments as specific biomarkers. Biogeosciences Discussions 2019, 1-24.

Laut, L., Vilar, A., Belart, P., Clemente, I., Fontana, L., Pereira, E., Ballalai, J., 2020. Organic matter compounds as a tool for trophic state characterization in a hypersaline environment: Araruama Lagoon, Brazil. Journal of South American Earth Sciences 97, 102403.

Lee, H., Galy, V., Feng, X., Ponton, C., Galy, A., France-Lanord, C., Feakins, S.J., 2019. Sustained wood burial in the Bengal Fan over the last 19 My. Proceedings of the National Academy of Sciences 116, 22518-22525.

Lee, J.S., Han, J.H., An, S.-U., Kim, S.-H., Lim, D., Kim, D., Kang, D.-J., Park, Y.-G., 2019. Sedimentary organic carbon budget across the slope to the basin in the southwestern Ulleung (Tsushima) Basin of the East (Japan) Sea. Journal of Geophysical Research: Biogeosciences 124, 2804-2822.

Maier, K.L., Rosenberger, K.J., Paull, C.K., Gwiazda, R., Gales, J., Lorenson, T., Barry, J.P., Talling, P.J., McGann, M., Xu, J., Lundsten, E., Anderson, K., Litvin, S.Y., Parsons, D.R., Clare, M.A., Simmons, S.M., Sumner, E.J., Cartigny, M.J.B., 2019. Sediment and organic carbon transport and deposition driven by internal tides along Monterey Canyon, offshore California. Deep Sea Research Part I: Oceanographic Research Papers 153, 103108.


Umhau, B.P., Benitez-Nelson, C.R., Close, H.G., Hannides, C.C.S., Motta, L., Popp, B.N., Blum, J.D., Drazen, J.C., 2019. Seasonal and spatial changes in carbon and nitrogen fluxes

estimated using 234Th:238U disequilibria in the North Pacific tropical and subtropical gyre. Marine Chemistry 217, 103705.

ATMOSPHERIC GEOCHEMISTRY


Grace, D.N., Sharp, J.R., Holappa, R.E., Lugos, E.N., Sebold, M.B., Griffith, D.R., Hendrickson, H.P., Galloway, M.M., 2019. Heterocyclic product formation in aqueous brown carbon systems. ACS Earth and Space Chemistry 3, 2472-2481.

Kirpes, R.M., Bonanno, D., May, N.W., Fraund, M., Barget, A.J., Moffet, R.C., Ault, A.P., Pratt, K.A., 2019. Wintertime Arctic sea spray aerosol composition controlled by sea ice lead microbiology. ACS Central Science 5, 1760-1767.

Maceira, A., Marcé, R.M., Borrull, F., 2020. Analytical methods for determining organic compounds present in the particulate matter from outdoor air. TrAC Trends in Analytical Chemistry 122, 115707.

Tong, H., Zhang, Y., Filippi, A., Wang, T., Li, C., Liu, F., Leppla, D., Kourtchev, I., Wang, K., Keskinen, H.-M., Levula, J.T., Arangio, A.M., Shen, F., Ditas, F., Martin, S.T., Artaxo, P., Godoi, R.H.M., Yamamoto, C.I., de Souza, R.A.F., Huang, R.-J., Berkemeier, T., Wang, Y., Su, H., Cheng, Y., Pope, F.D., Fu, P., Yao, M., Pöhlker, C., Petäjä, T., Kulmala, M., Andreae, M.O., Shiraiwa, M., Pöschl, U., Hoffmann, T., Kalberer, M., 2019. Radical formation by fine particulate matter associated with highly oxygenated molecules. Environmental Science & Technology 53, 12506-12518.

Vogel, A.L., Lauer, A., Fang, L., Arturi, K., Bachmeier, F., Daellenbach, K.R., Käser, T., Vlachou, A., Pospisilova, V., Baltensperger, U., Haddad, I.E., Schwikowski, M., Bjelić, S., 2019. A comprehensive nontarget analysis for the molecular reconstruction of organic aerosol composition from glacier ice cores. Environmental Science & Technology 53, 12565-12575.

HYDROSPHERE GEOCHEMISTRY



Bhattacharya, R., Osburn, C.L., 2020. Spatial patterns in dissolved organic matter composition controlled by watershed characteristics in a coastal river network: The Neuse River Basin, USA. Water Research 169, 115248.

Blattmann, T.M., Liu, Z., Zhang, Y., Zhao, Y., Haghipour, N., Montluçon, D.B., Plötze, M., Eglinton, T.I., 2019. Mineralogical control on the fate of continentally derived organic matter in the ocean. Science 366, 742-745.

Čanković, M., Žučko, J., Radić, I.D., Janeković, I., Petrić, I., Ciglenečki, I., Collins, G., 2019. Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake. Systematic and Applied Microbiology 42, 126016.

Coch, C., Juhls, B., Lamoureux, S.F., Lafrenière, M.J., Fritz, M., Heim, B., Lantuit, H., 2019. Comparisons of dissolved organic matter and its optical characteristics in small low and high Arctic catchments. Biogeosciences 16, 4535-4553.

Dai, G., Zhu, E., Liu, Z., Wang, Y., Zhu, S., Wang, S., Ma, T., Jia, J., Wang, X., Hou, S., Fu, P., Peterse, F., Feng, X., 2019. Compositional characteristics of fluvial particulate organic matter exported from the world's largest alpine wetland. Journal of Geophysical Research: Biogeosciences 124, 2709-2727.


El-Sayed, M.E.A., Khalaf, M.M.R., Rice, J.A., 2019. Isotherm and kinetic studies on the adsorption of humic acid molecular size fractions onto clay minerals. Acta Geochimica 38, 863-871.



Jiang, T., Wang, D., Meng, B., Chi, J., Laudon, H., Liu, J., 2020. The concentrations and characteristics of dissolved organic matter in high-latitude lakes determine its ambient reducing capacity. Water Research 169, 115217.

Klun, K., Falnoga, I., Mazej, D., Šket, P., Faganeli, J., 2019. Colloidal organic matter and metal(loid)s in coastal waters (Gulf of Trieste, northern Adriatic Sea). Aquatic Geochemistry 25, 179-194.


Liu, S., He, Z., Tang, Z., Liu, L., Hou, J., Li, T., Zhang, Y., Shi, Q., Giesy, J.P., Wu, F., 2020. Linking the molecular composition of autochthonous dissolved organic matter to

source identification for freshwater lake ecosystems by combination of optical spectroscopy and FT-ICR-MS analysis. Science of The Total Environment 703, 134764.

Lu, K., Liu, Z., 2019. Molecular level analysis reveals changes in chemical composition of dissolved organic matter from South Texas rivers after high flow events. Frontiers in Marine Science 6, 673. doi: 610.3389/fmars.2019.00673.


Nakaya, Y., Nakashima, S., Otsuka, T., 2019. Evaluation of kinetic competition among formation and degradation processes of dissolved humic-like substances based on hydrothermal reactions measured by ultraviolet-visible spectroscopy. Geochemical Journal 53, 407-414.

Ooki, A., Shida, R., Otsu, M., Onishi, H., Kobayashi, N., Iida, T., Nomura, D., Suzuki, K., Yamaoka, H., Takatsu, T., 2019. Isoprene production in seawater of Funka Bay, Hokkaido, Japan. Journal of Oceanography 75, 485-501.

Song, N., Bai, L., Xu, H., Jiang, H.-L., 2020. The composition difference of macrophyte litter-derived dissolved organic matter by photodegradation and biodegradation: Role of reactive oxygen species on refractory component. Chemosphere 242, 125155.


Wagner, S., Brandes, J., Spencer, R.G.M., Ma, K., Rosengard, S.Z., Moura, J.M.S., Stubbins, A., 2019. Isotopic composition of oceanic dissolved black carbon reveals non-riverine source. Nature Communications 10, 5064.


Wang, H., Li, Z., Zhuang, W.-E., Hur, J., Yang, L., Wang, Y., 2020. Spectral and isotopic characteristics of particulate organic matter in a subtropical estuary under the influences of human disturbance. Journal of Marine Systems 203, 103264.


Yan, Y., Bender, M.L., Brook, E.J., Clifford, H.M., Kemeny, P.C., Kurbatov, A.V., Mackay, S., Mayewski, P.A., Ng, J., Severinghaus, J.P., Higgins, J.A., 2019. Two-million-year-old snapshots of atmospheric gases from Antarctic ice. Nature 574, 663-666.

Zangrando, R., Zanella, V., Karroca, O., Barbaro, E., Kehrwald, N.M., Battistel, D., Morabito, E., Gambaro, A., Barbante, C., 2020. Dissolved organic matter in the deep

TALDICE ice core: A nano-UPLC-nano-ESI-HRMS method. Science of The Total Environment 700, 134432.


Zhang, J., Yu, Z., Jia, G., 2020. Cyclisation degree of tetramethylated brGDGTs in marine environments and its implication for source identification. Global and Planetary Change 184, 103043.


Zhou, Y., Zhou, L., He, X., Jang, K.-S., Yao, X., Hu, Y., Zhang, Y., Li, X., Spencer, R.G.M., Brookes, J.D., Jeppesen, E., 2019. Variability in dissolved organic matter composition and biolability across gradients of glacial coverage and distance from glacial terminus on the Tibetan Plateau. Environmental Science & Technology 53, 12207-12217.

SOIL GEOCHEMISTRY


Cotrufo, M.F., Ranalli, M.G., Haddix, M.L., Six, J., Lugato, E., 2019. Soil carbon storage informed by particulate and mineral-associated organic matter. Nature Geoscience 12, 989-994.



Kida, M., Kondo, M., Tomotsune, M., Kinjo, K., Ohtsuka, T., Fujitake, N., 2019. Molecular composition and decomposition stages of organic matter in a mangrove mineral soil with time. Estuarine, Coastal and Shelf Science 231, 106478.


Liu, Y., Ma, W., Kou, D., Niu, X., Wang, T., Chen, Y., Chen, D., Zhu, X., Zhao, M., Hao, B., Zhang, J., Yang, Y., Hu, H., 2019. How deep do we dig for surface soil? A comparison of patterns of microbial C:N:P stoichiometry between topsoil and subsoil along an aridity gradient. Biogeosciences Discussions 2019, 1-36.

Ngaba, M.J.Y., Hu, Y.-L., Bol, R., Ma, X.-Q., Jin, S.-F., Mgelwa, A.S., 2019. Effects of land use change from natural forest to plantation on C, N and natural abundance of 13C and 15N along a climate gradient in eastern China. Scientific Reports 9, 16516.

Reda, R., Saffaj, T., Ilham, B., Saidi, O., Issam, K., Brahim, L., El Hadrami, E.M., 2019. A comparative study between a new method and other machine learning algorithms for soil organic carbon and total nitrogen prediction using near infrared spectroscopy. Chemometrics and Intelligent Laboratory Systems 195, 103873.

Reusser, J.E., Verel, R., Zindel, D., Frossard, E., McLaren, T.I., 2019. Identification of lower-order inositol phosphates (IP5 and IP4) in soil extracts as determined by hypobromite oxidation and solution 31P NMR spectroscopy. Biogeosciences Discussions 2019, 1-28.


Zhang, P., Huang, P., Xu, X., Sun, H., Jiang, B., Liao, Y., 2019. Spectroscopic and molecular characterization of biochar-derived dissolved organic matter and the associations with soil microbial responses. Science of The Total Environment, 134619.


Remote Sensing-Hydrocarbon Seepage

Garain, S., Mitra, D., Das, P., 2019. Detection of hydrocarbon microseepage-induced anomalies by spectral enhancements of Landsat 7 ETM+ images in part of Assam–Arakan Fold Belt, India. Journal of Petroleum Exploration and Production Technology 9, 2573-2582.

Hsu, C.-W., MacDonald, I.R., Römer, M., Pape, T., Sahling, H., Wintersteller, P., Bohrmann, G., 2019. Characteristics and hydrocarbon seepage at the Challenger Knoll in the Sigsbee Basin, Gulf of Mexico. Geo-Marine Letters 39, 391-399.

Lazar, M., Gasperini, L., Polonia, A., Lupi, M., Mazzini, A., 2019. Constraints on gas release from shallow lake sediments—a case study from the Sea of Galilee. Geo-Marine Letters 39, 377-390.

Roelofse, C., Alves, T.M., Gafeira, J., 2020. Structural controls on shallow fluid flow and associated pockmark fields in the East Breaks area, northern Gulf of Mexico. Marine and Petroleum Geology 112, 104074.

Römer, M., Hsu, C.-W., Loher, M., MacDonald, I.R., dos Santos Ferreira, C., Pape, T., Mau, S., Bohrmann, G., Sahling, H., 2019. Amount and fate of gas and oil discharged at 3400 m water

depth from a natural seep site in the southern Gulf of Mexico. Frontiers in Marine Science 6, 700. doi: 710.3389/fmars.2019.00700.


Zhang, Y., Muxworthy, A.R., Jia, D., Wei, G., Xia, B., Wen, B., Wang, M., Liu, W., Brzozowski, M.J., 2019. Identifying and dating the destruction of hydrocarbon reservoirs using secondary chemical remanent magnetization. Geophysical Research Letters 46, 11100-11108.

Abstracts

Abplanalp, M.J., Frigge, R., Kaiser, R.I., 2019. Low-temperature synthesis of polycyclic aromatic hydrocarbons in Titan’s surface ices and on airless bodies. Science Advances 5, eaaw5841.

http://advances.sciencemag.org/content/5/10/eaaw5841.abstract

Titan’s equatorial dunes represent the most monumental surface structures in our Solar System, but the chemical composition of their dark organics remains a fundamental, unsolved enigma, with solid acetylene detected near the dunes implicated as a key feedstock. Here, we reveal in laboratory simulation experiments that aromatics such as benzene, naphthalene, and phenanthrene—prospective building blocks of the organic dune material—can be efficiently synthesized via galactic cosmic ray exposure of low-temperature acetylene ices on Titan’s surface, hence challenging conventional wisdom that aromatic hydrocarbons are formed solely in Titan’s atmosphere. These processes are also of critical importance in unraveling the origin and chemical composition of the dark surfaces of airless bodies in the outer Solar System, where hydrocarbon precipitation from the atmosphere cannot occur. This finding notably advances our understanding of the distribution of carbon throughout our Solar System such as on Kuiper belt objects like Makemake.

Abu-Mahfouz, I.S., Cartwright, J.A., Idiz, E., Hooker, J.N., Robinson, S., van den Boorn, S., 2019. Genesis and role of bitumen in fracture development during early catagenesis. Petroleum Geoscience 25, 371.

http://pg.lyellcollection.org/content/25/4/371.abstract

Bitumen-bearing fractures and vugs were investigated in the highly organic-rich Jordan oil shale (JOS) of Late Cretaceous–Eocene age, which has potential as a highly fractured, unconventional hydrocarbon play. Bitumen is present as macroscopically visible deposits, and as inclusions in the cement of abundant natural fractures and adjacent vugs. The frequency of bitumen occurrence in fractures closely correlates with total organic carbon (TOC) and burial depth. Petrographical and organic-geochemical analyses on bitumen samples extracted from fractures and their host-rock matrix show that the fracture-filling bitumen comprises indigenous low maturity hydrocarbons derived from the surrounding organic-rich oil shale and has not migrated from a deeper source. Maturity indicators imply that the oil shale is in the pre-oil generation stage of early catagenesis throughout the investigated area, but with a regional increase in thermal maturity from west to east as the result of greater maximum burial depth. Bitumen mobilization in the host rock was mainly controlled by vertical loading stress acting on the non-Newtonian bitumen phase in load-bearing configurations in the organic-rich matrix. Bitumen fractures were developed by hydraulic fracturing as the result of fluid overpressure in the organic matter. Overpressured bitumen has acted as a fracture driver, generating bitumen veins in both the organic-rich mudstones and the adjacent chert and silicified intervals.Supplementary material: A summary of core data and photographs of the fracture bitumen and matrix bitumen are available at

https://doi.org/10.6084/m9.figshare.c.4602290Thematic collection: This article is part of the Naturally Fractured Reservoirs collection available at: https://www.lyellcollection.org/cc/naturally-fractured-reservoirs

Adam, P.S., Borrel, G., Gribaldo, S., 2019. An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. Nature Microbiology 4, 2155-2163.

https://doi.org/10.1038/s41564-019-0534-2

The tetrahydromethanopterin (H4MPT) methyl branch of the Wood–Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy. It has been proposed that the H4MPT branch dates back to the last universal common ancestor. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear. Here, we have examined the distribution and phylogeny of the enzymes involved in the H4MPT branch and the biosynthesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood–Ljungdahl H4MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H4MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H4MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth’s history.

Agartan, E., Illangasekare, T.H., Vargas-Johnson, J., Cihan, A., Birkholzer, J., 2020. Experimental investigation of assessment of the contribution of heterogeneous semi-confining shale layers on mixing and trapping of dissolved CO2 in deep geologic formations. International Journal of Greenhouse Gas Control 93, 102888.

http://www.sciencedirect.com/science/article/pii/S1750583619303925

In most conceptual models of dissolution trapping of CO2, it is assumed that mixing of dissolved supercritical CO2 and formation brine occurs through density-driven convection. In our previous modeling study, we showed that the presence of continuous low-permeability shale layers in the formations causes convective shutdown through disruption of fingers, which impacts the effectiveness of mixing and trapping processes. However, these layers are naturally heterogeneous due to variations in compositional and textural properties. In the present study, we investigate the potential effects of heterogeneity present within semi-confining low-permeability layers on the overall mixing and trapping of dissolved CO2. Since accurate field experimentation in deep geologic formations is difficult due to inability to adequately characterize geology and define boundary conditions of the formation, we designed well-controlled experiments using NaBr solution and water under laboratory conditions. We conducted intermediate-scale 3D laboratory experiments under two homogeneous and one heterogeneous multilayered sand packing configurations. The results of these experiments show that connectivity of relatively higher permeability material within the semi-confining low-permeability layers contributes to mixing through (1) brine leakage between upper and lower aquifers (reverse convection), and (2) trapping through diffusion and back diffusion of initially trapped mass due to reversed concentration gradients in the long term. These findings suggest that when estimating the effectiveness of dissolution trapping in CO2 sequestration one needs to consider possible deviations from the traditional convective mixing theory in homogeneous media. Under some conditions of natural formation heterogeneity, diffusion can contribute to trapping; in some others, it may not.

Ahmed, O.E., Eldesoky, A.M., El Nady, M.M., 2019. Evaluation of petroleum hydrocarbons and its impact on organic matters of living organisms in the northwestern Gulf of Suez, Egypt. Petroleum Science and Technology 37, 2441-2449.

https://doi.org/10.1080/10916466.2019.1655443

The levels of Total Petroleum Hydrocarbons (TPH) have been reported for ten commercially important fish species from the northwestern Gulf of Suez, Egypt. Target compounds were analytically determined with gas chromatography–flame ionization detector and High-performance liquid chromatography analysis. Results showed that total petroleum hydrocarbon varied from 21700 to 1503100 ng/g wet wt., Argyrops Spinifer showed the highest level of TPH in the muscle tissue followed by Euthynnus affinis 1459800 ng/g wet wt. These data are very important for coming pollution monitoring program to the Suez Gulf. Polycyclic aromatic hydrocarbons (16 PAHs) varied between 81.499 and 5895.608 ng/g wet wt. The diagnostic indices used showed that the hydrocarbons in the area were from both biogenic and anthropogenic sources. Hence, there is need for adequate regulation and control of all activities contributing to the levels of petroleum hydrocarbon in the marine environment for the safety of human, and fish species lives in the area.

Ai, J.Y., George, S.C., Zhong, N.N., 2020. Organic geochemical characteristics of highly mature Late Neoproterozoic black shales from South China: Reappraisal of syngeneity and indigeneity of hydrocarbon biomarkers. Precambrian Research 336, 105508.


During the Late Neoproterozoic to early Cambrian period, the transition from mainly microbial ecosystems to eukaryotic marine primary productivity was one of the most profound ecological revolutions in Earth’s history. Abundant biomarkers have been reported from high maturity Late Neoproterozoic sedimentary rocks in South China, including the Cryogenian Datangpo and Ediacaran Doushantuo formations. These biomarkers were suggested to be organic molecular evidence of the survival of photosynthetic eukaryotes in palaeo-oceanic environments during the Snowball Earth era. To advance the understanding of Late Neoproterozoic ecosystems and to re-evaluate the provenance and validity of the biomarkers, fresh drill core was collected from black shales of the Datangpo and Doushantuo formations in South China. In order to ensure the indigeneity of the solvent extracted hydrocarbons, their composition was determined by conducting experiments under strict laboratory procedures, including using slice experiments on a precision saw that removed external surfaces. The distribution of the recovered aliphatic and aromatic hydrocarbons indicates very a high thermal maturity for the analysed black shales, which is consistent with the equivalent vitrinite reflectance (~2.5%) and the lack of specific biomarkers. Both prokaryotic (bacterial) and eukaryotic (algal) organisms are likely producers during the Neoproterozoic. However, no long-chain steranes (≥C26 steranes) were detected in the interior of any of the samples, and only trace amounts of hopanes and pregnanes in just one sample from the Doushantuo Formation (xs-199-DST). On the contrary, solvent extraction of millimetre-thick slices cut from the external surfaces of the black shales reveals strikingly high level of contamination from organic residues on the sample surfaces. These contaminants include n-alkanes (C10 ~ C33), isoprenoids, monomethylalkanes, aromatic hydrocarbons (naphthalene, phenanthrene and their alkyl isomers) and abundant biomarkers such as tricyclic terpanes, hopanes, steranes and diasteranes. The concentrations of these biomarkers in the exterior sub-samples exceed blank concentrations by more than three orders of magnitude due to surficial contamination. These results indicate that previously studied Late Neoproterozoic samples from South China likely contain mixtures of abundant biomarker contaminants and some indigenous over-mature hydrocarbons. Therefore, special care need to be taken with regard the existing biomarker evidence from South China that has been used to illustrate the contribution of eukaryotic photosynthesis to marine primary productivity during the Snowball Earth period. No Late Neoproterozoic rocks from South China within the appropriate thermal maturity window for survival of indigenous biomarkers are currently known, but these may be found during future exploration.


https://doi.org/10.1007/s11242-019-01336-5

We demonstrate how to use numerical simulation models directly on micro-CT images to understand the impact of several enhanced oil recovery (EOR) methods on microscopic displacement efficiency. To describe the physics

with high-fidelity, we calibrate the model to match a water-flooding experiment conducted on the same rock sample (Akai et al. in Transp Porous Media 127(2):393–414, 2019. https://doi.org/10.1007/s11242-018-1198-8). First we show comparisons of water-flooding processes between the experiment and simulation, focusing on the characteristics of remaining oil after water-flooding in a mixed-wet state. In both the experiment and simulation, oil is mainly present as thin oil layers confined to pore walls. Then, taking this calibrated simulation model as a base case, we examine the application of three EOR processes: low salinity water-flooding, surfactant flooding and polymer flooding. In low salinity water-flooding, the increase in oil recovery was caused by displacement of oil from the centers of pores without leaving oil layers behind. Surfactant flooding gave the best improvement in the recovery factor of 16% by reducing the amount of oil trapped by capillary forces. Polymer flooding indicated improvement in microscopic sweep efficiency at a higher capillary number, while it did not show an improvement at a low capillary number. Overall, this work quantifies the impact of different EOR processes on local displacement efficiency and establishes a workflow based on combining experiment and modeling to design optimal recovery processes.



Extraction of adamantanes and diamantanes from petroleum source rock using nonionic surfactant was investigated and the optimum conditions for yields of the diamondoids were determined. The conventionally used accelerated solvent extraction method was compared to an innovative microwave-assisted nonionic surfactant extraction (MANSE). A three-level full factorial design of experiment (DoE) was adopted for the optimization of MANSE, involving solvent concentration, extraction temperature as well as extraction time. In-tube extraction (ITEX-2) using TENAX TA as sorbent in combination with gas chromatography-mass spectrometry (GC-MS) was used to determine the diamondoids in the extract. The results revealed that solvent concentration, extraction temperature and time have significant effects on extraction yields of the diamondoids. 0.04 M was the optimum surfactant concentration for extraction of both, adamantane and diamantane. The highest yields of the diamondoids were obtained at extraction temperature of 80 °C. The optimum extraction time for both adamantane and diamantane was 10 min. In comparison with the accelerated solvent extraction method, the results showed that MANSE is more efficient. This study has revealed that MANSE is a robust and efficient environmentally benign sample preparation method for geochemical evaluation of petroleum source rock.

Akri, M., Zhao, S., Li, X., Zang, K., Lee, A.F., Isaacs, M.A., Xi, W., Gangarajula, Y., Luo, J., Ren, Y., Cui, Y.-T., Li, L., Su, Y., Pan, X., Wen, W., Pan, Y., Wilson, K., Li, L., Qiao, B., Ishii, H., Liao, Y.-F., Wang, A., Wang, X., Zhang, T., 2019. Atomically dispersed nickel as coke-resistant active sites for methane dry reforming. Nature Communications 10, 5181.

https://doi.org/10.1038/s41467-019-12843-w

Dry reforming of methane (DRM) is an attractive route to utilize CO2 as a chemical feedstock with which to convert CH4 into valuable syngas and simultaneously mitigate both greenhouse gases. Ni-based DRM catalysts are promising due to their high activity and low cost, but suffer from poor stability due to coke formation which has hindered their commercialization. Herein, we report that atomically dispersed Ni single atoms, stabilized by interaction with Ce-doped hydroxyapatite, are highly active and coke-resistant catalytic sites for DRM. Experimental and computational studies reveal that isolated Ni atoms are intrinsically coke-resistant due to their unique ability to only activate the first C-H bond in CH4, thus avoiding methane deep decomposition into carbon. This discovery offers new opportunities to develop large-scale DRM processes using earth abundant catalysts.

Al-Mudhafar, W.J., 2019. Polynomial and nonparametric regressions for efficient predictive proxy metamodeling: Application through the CO2-EOR in shale oil reservoirs. Journal of Natural Gas Science and Engineering 72, 103038.


An integrated optimization workflow combining Particle Swarm and Non-parametric Proxy Metamodels was adopted with reservoir simulation to optimize oil production in CO2-EOR in shale oil reservoirs. The cyclic-CO2 flooding optimization consisted of injection, soaking, and production durations over the prediction period. Also, Minimum bottom hole pressure, maximum oil production rate, and water cut were optimized for the production wells, and maximum bottom hole injection pressure and maximum gas injection rate were optimized for the injection wells. To reach the optimal solution, 176-candidate solutions were created as training experiments with 4 successive iterations of approximately 20 experiments each. The optimal solution increased oil production by 322,675 surface barrels. Next, a 2nd order polynomial regression, Multivariate Adaptive Regression Splines and Random Forest Model proxy models were constructed to metamodel the large reservoir simulator. The polynomial proxy has the least prediction error among other approaches to simplify the reservoir evaluation and optimization process.

Al Maskari, N.S., Saeedi, A., Xie, Q., 2019. Alcohol-assisted waterflooding in carbonate reservoirs. Energy & Fuels 33, 10651-10658.

https://doi.org/10.1021/acs.energyfuels.9b02497

Low-salinity waterflooding has been identified as a cost-effective and environmentally friendly means to enhance oil recovery in carbonate reservoirs by decreasing hydrophobicity. Published work shows that a low concentration of 1-pentanol can further decrease the hydrophobicity, although the mechanism(s) remain unclear. In this work, we aimed to decipher the controlling factor(s), which prevail the process of wettability alteration, by adding alcohols in injected water. To achieve this aim, we examined the effect of alcohol carbon chain length and number of −OH functional groups on the contact angle of oil–brine–carbonate using ethanol, isopropanol, 1-pentanol, and glycerol in high- and low-salinity brines. Moreover, to interpret the contact angle results on the basis of a thermodynamic isotherm, we measured the ζ potential of brine–calcite and brine–oil with and without alcohols at ambient conditions. Contact angle results confirm that intermediate carbon chain alcohol (1-pentanol) shifts the wettability of the oil–brine–carbonate system to less oil-wet or more water-wet, implying greater hydrophilicity compared to other short carbon chain alcohols. Also, the number of −OH functional groups in an alcohol has a negligible effect on the contact angle and, thus, wettability alteration. However, the ζ potential at oil–brine and brine–calcite fails to explain the effect of alcohols on the wettability of the oil–brine–carbonate system, implying that the Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory may not account for the effect of alcohol on the wettability alteration. We argue that increasing the length of the carbon chain likely increases −OH at oil–brine interfaces, which likely breaks the in situ bridges between oil and calcite surfaces, thus increasing hydrophilicity. Our finding shows that waterflooding efficiency may be boosted by adding 1-pentanol with a low concentration in high-salinity carbonate reservoirs, where conventional chemical-assisted enhanced oil recovery (e.g., polymer flooding and surfactant flooding) may not be viable.



We study in situ three-phase near-miscible CO2 injection in a water-wet carbonate rock at elevated temperature and pressure using X-ray microtomography. We examine the recovery mechanisms, presence or absence of oil layers, pore occupancy and interfacial areas during a secondary gas injection process. In contrast to an equivalent immiscible system, we did not observe layers of oil sandwiched between gas in the centre of the pore space and water in the corners. At near-miscible conditions, the measured contact angle between oil and gas was approximately 73°, indicating only weak oil wettability in the presence of gas. Oil flows in the centres of large pores, rather than in layers for immiscible injection, when displaced by gas. This allows for a rapid production of oil since it is no longer confined to movement in thin layers. A significant recovery factor of 80% was obtained and the residual oil saturation existed as disconnected blobs in the corners of the pore space. At

equilibrium, gas occupied the biggest pores, while oil and water occupied pores of varying sizes (small, medium and large). Again, this was different from an immiscible system, where water occupied only the smallest pores. We suggest that a double displacement mechanism, where gas displaces water that displaces oil is responsible for shuffling water into larger pores than that seen after initial oil injection. This is only possible since, in the absence of oil layers, gas can contact water directly. The gas-oil and oil-water interfacial areas are lower than in the immiscible case, since there are no oil layers and even water layers in the macro-pore space become disconnected; in contrast, there is a larger direct contact of oil to the solid. These results could serve as benchmarks for developing near-miscible pore-scale modelling tools.

Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., Mashaghi, A., Hankemeier, T., 2019. Single-cell metabolomics by mass spectrometry: advances, challenges, and future applications. TrAC Trends in Analytical Chemistry 120, 115436.


Cellular heterogeneity is a phenomenon that is often observed but poorly understood. Single-cell metabolomics can provide insights into the phenotypical variations between individual cells. Recent advances in microfluidics, micromanipulation, image analysis, and automation allowed for high-throughput isolation of single cells in a minimally disruptive manner as to not affect the cell metabolism. Coupled with new innovations in mass spectrometry-based analytical techniques, single cell metabolomics stands at the cusp of becoming an established field. In this review, some of the recent single cell isolation platforms that are especially suited for metabolomics will be highlighted, as well as the recent trends in mass spectrometry-based single cell platforms. Additionally, some of the limitations of single-cell metabolomics and its recent applications will be briefly discussed.

Alipour, M., Alizadeh, B., Chehrazi, A., Mirzaie, S., 2019. Combining biodegradation in 2D petroleum system models: application to the Cretaceous petroleum system of the southern Persian Gulf basin. Journal of Petroleum Exploration and Production Technology 9, 2477-2486.

https://doi.org/10.1007/s13202-019-0716-8

Biodegradation modeling is combined with petroleum system modeling along a regional 2D transect from the southern Persian Gulf basin. An advanced basement model was considered in the model that allowed a constant temperature to enter the entire sedimentary column. Modeling results were calibrated against existing temperature and vitrinite reflectance data from nearby wells. Temperature, burial, and charge histories are carefully monitored within the studied section through geological time. Based on our modeling results, biodegradation has been effective along the migration pathway and within the eventual accumulation sites to varying extents. These findings can have practical implications for pre-drill oil quality predictions and accurate geochemical evaluations of oils and reduce offshore oil and gas exploration risks.

Alleon, J., Flannery, D.T., Ferralis, N., Williford, K.H., Zhang, Y., Schuessler, J.A., Summons, R.E., 2019. Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments. Scientific Reports 9, 16712.

https://doi.org/10.1038/s41598-019-53272-5

Hydrothermal and metamorphic processes could have abiotically produced organo-mineral associations displaying morphological and isotopic characteristics similar to those of fossilized microorganisms in ancient rocks, thereby leaving false-positive evidence for early life in the geological record. Recent studies revealed that geologically-induced alteration processes do not always completely obliterate all molecular information about the original organic precursors of ancient microfossils. Here, we report the molecular, geochemical, and mineralogical composition of organo-mineral associations in a chert sample from the ca. 3.47 billion-year-old (Ga) Mount Ada Basalt, in the Pilbara Craton, Western Australia. Our observations indicate that the molecular characteristics of carbonaceous matter are consistent with hydrothermally altered biological organics, although

significantly distinct from that of organic microfossils discovered in a chert sample from the ca. 3.43 Ga Strelley Pool Formation in the same area. Alternatively, the presence of native metal alloys in the chert, previously believed to be unstable in such hydrothermally influenced environments, indicates strongly reducing conditions that were favorable for the abiotic formation of organic matter. Drawing definitive conclusions about the origin of most Paleoarchean organo-mineral associations therefore requires further characterization of a range of natural samples together with experimental simulations to constrain the molecular composition and geological fate of hydrothermally-generated condensed organics.

Alnahwi, A., Loucks, R.G., 2019. Mineralogical composition and total organic carbon quantification using x-ray fluorescence data from the Upper Cretaceous Eagle Ford Group in southern Texas. American Association of Petroleum Geologists Bulletin 103, 2891-2907.

http://archives.datapages.com/data/bulletns/2019/12dec/BLTN18090/bltn18090.html

Six southern Texas Eagle Ford cores were investigated to quantify mineralogical composition and total organic carbon (TOC). Machine learning of the x-ray fluorescence (XRF) data set was conducted using neural network analysis to predict mineralogies for L1, L2, and L3 and TOC for L1, L2, L3, Iona-1, Innes-1, and well “X.” Inees-1 and well “X” were used as blind tests to check the quality of the developed models. The online Neural Designer software was used to perform the training process and develop models. Quantitative laboratory-measured x-ray diffraction (XRD) mineralogies and TOC were used to conduct the training and develop high-resolution semiquantitative models, and the derived mineralogic and organic matter models were found to be promising. The modeled mineralogy and TOC represent continuous relative abundances, which are far more significant than scattered individual XRD and TOC point measurements. The significance of this study is that it allows for the use of relatively inexpensive and nondestructive XRF analysis that requires minimal sample preparation to construct high-resolution mineral abundances and TOC content. With modern advances in technology, XRF can now be measured on drill cuttings in real time while drilling is occurring, allowing operators to use the proposed method to construct semiquantitative mineralogical and TOC models for evaluating placement of laterals in prospective intervals and designing completion techniques accordingly.

Álvaro, J.J., Cortijo, I., Jensen, S., Martí Mus, M., Palacios, T., 2020. Cloudina-microbial reef resilience to substrate instability in a Cadomian retro-arc basin of the Iberian Peninsula. Precambrian Research 336, 105479.


The Navalpino anticline of the Central Iberian Zone provides a unique case study of well-exposed late Ediacaran reefs. Drone images show their spatial arrangement as tens of shelly-microbial patch, biohermal and complex reefs encased in a dominantly shaly succession. The latter was deposited on a perturbed block-platform located in a Cadomian retro-arc basin fringing West Gondwana. Reefs display the traditional core/flank/inter-reef subdivision and developed on generally low-energy, clear-water substrates, between normal and storm wave base. Cores consist of millimetre-sized irregular mesoclots of dense microbial microsparite, locally interrupted by laminated (stromatolitic) fabrics, containing abundant Sinotubulites and Cloudina shells, the last with upright preservation. Basement breakdown perturbations related to fissuring, hydrothermal influence and slope-apron breccia deposition led to nucleation and development of patch-reefs on unstable substrates. Their ecological succession is characterized by stabilization (pioneer)-to-colonization phases, the latter represented by Cloudina shells preserved upright and encased in microbial crusts, pointing to their active role as pioneer frame-building taxa.


https://doi.org/10.1038/s41561-019-0455-y

Northern peatlands store over 1,000 Gt of carbon, almost double previous estimates, according to a new analysis of peat core data. The fate of this peat carbon, however, is uncertain in a rapidly changing world.

Amin, J.S., Kuyakhi, H.R., Bahadori, A., 2019. Intelligent prediction of aliphatic and aromatic hydrocarbons in Caspian Sea sediment using a neural network based on particle swarm optimization. Petroleum Science and Technology 37, 2364-2373.

https://doi.org/10.1080/10916466.2018.1542439

tIn this paper an intelligent model is proposed to predict the amount of organic pollutants in Caspian Sea sediment based on a feed forward artificial neural network (ANN) optimized by particle swarm optimization (PSO) algorithm. Organic pollutants have carcinogenesis and mutagenesis properties which are derived from anthropogenic and natural sources. The PSO-ANN was developed by experimental data collected from different literature. The statistical parameters prove the satisfactory performance of the proposed PSO- ANN model. A good correlation was obtained between the predicted organic pollutants and the experimental data for test, train and validation data were 0.996, 0.997, 0.993, respectively.

Amrouche, F., Gomari, S.R., Islam, M., Donglai, X., 2019. New insights into the application of a magnetic field to enhance oil recovery from oil-wet carbonate reservoirs. Energy & Fuels 33, 10602-10610.


Given recent moves toward cleaner energy production, the application of environmentally friendly methods for enhanced oil recovery (EOR) is considered to be an important research strategy in increasing oil production from existing hydrocarbon reservoirs. Therefore, in this article, the application of a magnetic field is introduced for the first time as a novel and eco-friendly EOR technique for oil-wet carbonate reservoirs. The magnetic field is generated using three different magnet strengths of 3000, 4100, and 6000 Gauss (G). The impact of incremental increases in the magnetic field on oil production from Austin chalk is investigated through measurements of the contact angle (CA), rock compaction, spontaneous imbibition (SI) of water, and the monitoring of the rock surface streaming potential. Dynamic CA measurements on oil-wet chalk surfaces in the presence of a magnetic field show that the value of CA is reduced faster than when a magnetic field is absent, indicating a significant increase in water imbibition into rock pores. The results of SI tests reveal significantly greater oil production during the imbibition process in the presence of a magnetic field at about 8.5 times that from oil-wet chalk. Monitoring the streaming potential of the oil-wet rock surface in the presence and absence of a magnetic field indicates that a change in the surface potential charge is responsible for the change in wettability of the surface from oil-wet to water-wet, hence improving water imbibition into carbonate rock which, in turn, can improve the oil displacement from pores.

Andersen, S.I., 2019. Petroleum size exclusion chromatography: Mechanisms explaining the NMP front peak. Energy & Fuels 33, 10667-10677.


Size exclusion chromatography (SEC) is abundantly used in analysis and fractionation of petroleum fractions despite numerous challenges with the techniques. Changing the eluent type among classical solvents in SEC normally leads to smaller changes in the elution profile of asphaltenes. Changing the eluent to N-methyl pyrrolidone (NMP) however leads to very different chromatographic profiles. Especially, the occurrence of a very early eluting peak has been severely debated in the literature without reaching a clear conclusion. NMP has particular solvent properties that target the solubility of aromatic molecules, and therefore asphaltenes are only partially soluble. In order to understand the occurrence of the front peak in NMP a systematic study is undertaken by changing eluent solvents and temperature. We discuss the different mechanisms involved in SEC such as phase behavior, gel swelling, pore size, molecular size, and unwanted adsorption that are all involved in the chromatographic process. To investigate the phase behavior and effects of reduced solubility, the elution in mixtures of heptane and toluene is presented. This leads to an increase adsorption but no indication of larger-sized aggregates as could have been expected. Analysis of the difference between NMP, THF, and toluene profiles indicate that gel swelling and void volume variation are relatively insignificant and cannot explain the

early peak. This therefore points at a different mechanism based on fluid dynamic effects known from hydrodynamic chromatography (HDC) of particles where larger particles travel faster than the average fluid velocity in a laminar flow and arrive at the detector before the average void volume. Based on the observations on petroleum systems in NMP, we therefore hypothesize that HDC is the driver behind the appearance of the peak in NMP. The insights revealed by the present study show that SEC can be used also to understand changes in solubility in the eluent solvent, for example, caused by alteration in chemistry.

Anto, S., Mukherjee, S.S., Muthappa, R., Mathimani, T., Deviram, G., Kumar, S.S., Verma, T.N., Pugazhendhi, A., 2020. Algae as green energy reserve: Technological outlook on biofuel production. Chemosphere 242, 125079.


Depletion of fossil fuel sources and their emissions have triggered a vigorous research in finding alternative and renewable energy sources. In this regard, algae are being exploited as a third generation feedstock for the production of biofuels such as bioethanol, biodiesel, biogas, and biohydrogen. However, algal based biofuel does not reach successful peak due to the higher cost issues in cultivation, harvesting and extraction steps. Therefore, this review presents an extensive detail of deriving biofuels from algal biomass starting from various algae cultivation systems like raceway pond and photobioreactors and its bottlenecks. Evolution of biofuel feedstocks from edible oils to algae have been addressed in the initial section of the manuscript to provide insights on the different generation of biofuel. Different configuration of photobioreactor systems used to reduce contamination risk and improve biomass productivity were extensively discussed. Photobioreactor performance greatly relies on the conditions under which it is operated. Hence, the importance of such conditions alike temperature, light intensity, inoculum size, CO2, nutrient concentration, and mixing in bioreactor performance have been described. As the lipid is the main component in biodiesel production, several pretreatment methods such as physical, chemical and biological for disrupting cell membrane to extract lipid were comprehensively reviewed and presented. This review article had put forth the recent advancement in the pretreatment methods like hydrothermal processing of algal biomasses using acid or alkali. Eventually, challenges and future dimensions in algal cultivation and pretreatment process were discussed in detail for making an economically viable algal biofuel.

Antonio, M.L., Gao, Z., Moots, H.M., Lucci, M., Candilio, F., Sawyer, S., Oberreiter, V., Calderon, D., Devitofranceschi, K., Aikens, R.C., Aneli, S., Bartoli, F., Bedini, A., Cheronet, O., Cotter, D.J., Fernandes, D.M., Gasperetti, G., Grifoni, R., Guidi, A., La Pastina, F., Loreti, E., Manacorda, D., Matullo, G., Morretta, S., Nava, A., Fiocchi Nicolai, V., Nomi, F., Pavolini, C., Pentiricci, M., Pergola, P., Piranomonte, M., Schmidt, R., Spinola, G., Sperduti, A., Rubini, M., Bondioli, L., Coppa, A., Pinhasi, R., Pritchard, J.K., 2019. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science 366, 708-714.

http://science.sciencemag.org/content/366/6466/708.abstract

Abstract: Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome’s population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.

Editors Summary: A 10,000-year transect of Roman populations. Rome wasn't built (or settled) in a day. Antonio et al. performed an ancestral DNA analysis to investigate the genetic changes that occurred in Rome and central Italy from the Mesolithic into modern times. By examining 127 Roman genomes and their archaeological context, the authors demonstrate a major ancestry shift in the Neolithic between hunter gatherers and farmers. A second ancestry shift is observed in the Bronze Age, likely coinciding with trade and an increased movement of populations. Genetic changes track the historical changes occurring in Rome and reflect gene flow from across the Mediterranean, Europe, and North Africa over time.



The coal metamorphism, as it evolves the microstructure of the coals, would also have significant influences on the structural transformations and isotopic discriminations of the primary chemical moieties. The present study aims to illustrate the nitrogen functionalities present within the chemical framework of the bituminous coal samples from the Raniganj and the Jharia Basins and anthracite A samples of the fold-thrust belts of the Sikkim Himalayas as well as to document the metamorphic transformations of these nitrogenous moieties with the advent in the degree of the coalification. The stable carbon (−24.08 to −21.67‰ for bituminous coal samples and −23.91 to −21.39‰ for anthracite A samples) and nitrogen isotopes (1.64–2.81‰ for the bituminous coal samples; 1.07–3.44‰ for the anthracite A samples) do not show any significant variation with the vitrinite reflectance and, therefore, correspond to the terrestrial higher plant sources of the organic matter. Further, the weak shifts of stable nitrogen isotope values in the anthracite A samples may be attributed to the preservation of the organic nitrogen in the thermally stable aromatic and heterocyclic structures. The total organic carbon to total nitrogen (TOC/TN) ratio may represent the vascular organic matter input into the mire in the case of bituminous coal samples (33.49–43.69), while for the anthracite A samples, this ratio may be an indication of the preservation of the organic nitrogen in the stable chemical framework within the microstructure. The primary alteration of the labile nitrogen-containing groups including the pyrrolic structures would have been initiated by the aqueous fluid entering into the reactive chemical framework during hydrothermal metamorphism. During these processes, most of the nitrogen atoms would have been quaternarized, which is evidenced by strong correlation (r = 0.96) between the relative area ratio of the graphitic to pyrrolic nitrogen and the mean random vitrinite reflectance. Moreover, the intensity and relative area ratio of the pyridinic to pyrrolic nitrogen are strongly correlated with the mean random vitrinite reflectance (r = 0.92 and 0.89, respectively) suggesting entanglement of the nitrogen atoms within the pyridinic forms as well with increasing metamorphic temperature. These structural rearrangements would have intensified the cyclazine structures and preserved the pyridinic forms in the anthracite A samples. Due to the increase in aromaticity and consequent increase in surface hydrophobicity and decrease in the interlayer spacing, the fluid would have lost its mobile phase and could not invade the relatively inert aromatic clusters. Thus, the organic nitrogen atoms were preserved within the thermochemically stable functionalities without showing any substantial isotopic variation. The scientific contribution of this present investigation, hence, lies in depicting the transformation of organic nitrogen among the pyrrolic, pyridinic and the cyclazine moieties with insignificant shifts in stable nitrogen isotope during coalification.

Aoyagi, S., Kodama, Y., Passarelli, M.K., Vorng, J.-L., Kawashima, T., Yoshikiyo, K., Yamamoto, T., Gilmore, I.S., 2019. OrbiSIMS imaging identifies molecular constituents of the perialgal vacuole membrane of Paramecium bursaria with symbiotic Chlorella variabilis. Analytical Chemistry 91, 14545-14551.

https://doi.org/10.1021/acs.analchem.9b03571

The protist (mostly single-celled organisms), Paramecium bursaria, forms an intracellular symbiotic relationship with the single-celled algae, Chlorella variabilis, where P. bursaria provides nutrients (i.e., Ca2+, Mg2+, and K+), carbon dioxide for photosynthesis and protection from viruses, while C. variabilis provides oxygen, carbon fixation, and nutrients. Key to this successful relationship is the perialgal vacuole (PV) membrane, which surrounds C. variabilis and protects it from digestion by P. bursaria. The membrane is fragile and difficult to analyze using conventional methods therefore very little is known about the molecular composition. We used the OrbiSIMS, a new high-resolution mass spectrometer with subcellular resolution imaging, to study the compartmentalization of endosymbionts and elucidate biomolecular interactions between the host and endosymbiont. Ions from the region of interest, close to C. variabilis, and specific to the target samples containing PVs were found based on the chemical mapping and masses of the ions. We show chemical localizations of oligosaccharides in close proximity of C. variabilis endosymbionts in P. bursaria. These

oligosaccharides are detected in host-endosymbiont samples containing PV membrane-bound algae and absent in free-living algae and digestive vacuole (DV) membrane-bound algae in P. bursaria.

Arellano, A.R., Bianchi, T.S., Osburn, C.L., D'Sa, E.J., Ward, N.D., Oviedo-Vargas, D., Joshi, I.D., Ko, D.S., Shields, M.R., Kurian, G., Green, J., 2019. Mechanisms of organic matter export in estuaries with contrasting carbon sources. Journal of Geophysical Research: Biogeosciences 124, 3168-3188.

https://doi.org/10.1029/2018JG004868

Modifications in land use and climate will result in shifts in the magnitude and composition of organic matter (OM) transported from wetlands to coastal waters, but differentiation between riverine and wetland OM sources in coastal areas remains a challenge. Here, we evaluate particulate and dissolved OM export dynamics in two representative estuary geomorphologies—Apalachicola Bay (AP) and Barataria Bay (BB), characterized primarily by blackwater river inputs and high particle abundance, respectively. The magnitude and composition of OM exported from each estuary was evaluated based on seasonal measurements of surface water dissolved organic carbon (DOC), particulate organic carbon (POC), particulate nitrogen, the stable isotopic composition of DOC and POC, dissolved and particulate lignin phenols, and carbon‐normalized dissolved lignin‐phenol yields. Data and discriminant analyses support the initial hypothesis; AP is dominated by a more terrestrial source of OM due to importance of fluvial dissolved OM inputs, while BB is a more particle‐rich and wetland carbon‐dominated system. Total lignin export (sum of mean dissolved and mean particulate) was higher in BB (5.73 ± 2.50 × 105 kg/year) than in AP (4.21 ± 2.35 × 105 kg/year). Particulate lignin export from BB was greater than the export of dissolved lignin at either BB or AP, suggesting coastal marsh erosion may be driving this comparatively large export of particulate lignin. These data have important implications for the stability of stored OM in coastal habitats, particularly since such habitats in this region are highly vulnerable due to relative sea level rise.

Arnold, T.E., Brenner, M., Kenney, W.F., Bianchi, T.S., 2019. Recent trophic state changes of selected Florida lakes inferred from bulk sediment geochemical variables and biomarkers. Journal of Paleolimnology 62, 409-423.

https://doi.org/10.1007/s10933-019-00096-y

Short sediment cores (80–100 cm) from three Florida (USA) lakes (Sheelar, Wauberg, and Apopka) that range in trophic status, were analyzed for total organic carbon (TOC), total nitrogen, stable isotopes of organic carbon (δ13CTOC) and biomarkers (n-alkanes and fatty acids), to identify the sources of organic matter in the lake deposits, and to link changes in primary productivity to anthropogenic activities during the last ~ 150 years. Relatively small (0.07 km2), ultra-oligotrophic Lake Sheelar is located in a state park, and sediment analyses indicate stable trophic status in the water body since at least the middle of the nineteenth century. Algal biomarkers are in low abundance throughout the core and terrestrial lipids and δ13CTOC values suggest that vascular plants were the primary source of TOC to the lake sediments during the period of record. In larger, eutrophic Lakes Wauberg (1.5 km2) and Apopka (125 km2), algal-derived biomarkers increase in recent sediments, whereas δ13CTOC values and concentrations of terrestrial biomarkers decrease toward the sediment surface. Increasing dominance through time of autochthonous carbon sources in the Lake Wauberg and Apopka sediment records coincides with specific anthropogenic activities in the respective watersheds. Submersed macrophytes in Lake Wauberg were replaced by algal communities in the mid-1980s, following expansion of residential development in the watershed. Biomarker data from the Lake Apopka core show there was an abrupt transition in the lake in the late 1940s, from domination by vascular plants to domination by algae, which has been documented by other paleolimnological studies that used alternative trophic state indicators. The trophic state shift in Lake Apopka corresponds to a period of increased nutrient input to the lake, associated with extensive farming along the north shore. Florida lakes have experienced different trophic state trajectories over the last ~ 150 years, driven by specific human activities in their respective watersheds.

Atar, E., März, C., Schnetger, B., Wagner, T., Aplin, A., 2019. Local to global controls on the deposition of organic-rich muds across the Late Jurassic Laurasian Seaway. Journal of the Geological Society 176, 1143.

http://jgs.lyellcollection.org/content/176/6/1143.abstract

Muds deposited in large-scale epicontinental seaways provide deep insights into palaeoclimates, biogeochemical cycles, sedimentation processes and organic carbon burial during exceptionally warm periods throughout the Phanerozoic. Temporal changes can be monitored at single locations but the key, larger scale oceanographical and related biogeochemical processes are likely to be more clearly revealed by comparisons between individual sub-basins within seaways. Here, we compare inorganic geochemical records from the Jurassic (upper Pectinatites wheatleyensis to lower Pectinatites pectinatus ammonite zones) of the Swanworth Quarry 1 Core from the Wessex Basin (Dorset, UK) to time-equivalent records from the Ebberston 87 Core in the Cleveland Basin (Yorkshire, UK), 400 km apart. Our synthesis shows that while the Dorset sediments were deposited in an energetically more dynamic setting than the Yorkshire sediments, the overarching climatic and oceanographical processes responsible for variations in organic carbon enrichment and sedimentation were similar. Intervals of coeval organic carbon-rich sedimentation occurred in both basins, and a particulate shuttle was intermittently active in both basins. Consistent with recent climate simulations, we conclude that tropical climate conditions, associated with enhanced nutrient supply, were key drivers of sedimentation between the Jurassic Wessex and Cleveland Basins.Supplementary material: Geochemical data discussed in the manuscript is available at: https://doi.org/10.6084/m9.figshare.c.4531532

Athanasakoglou, A., Kampranis, S.C., 2019. Diatom isoprenoids: Advances and biotechnological potential. Biotechnology Advances 37, 107417.

http://www.sciencedirect.com/science/article/pii/S073497501930117X

Diatoms are among the most productive and ecologically important groups of microalgae in contemporary oceans. Due to their distinctive metabolic and physiological features, they offer exciting opportunities for a broad range of commercial and industrial applications. One such feature is their ability to synthesize a wide diversity of isoprenoid compounds. However, limited understanding of how these molecules are synthesized have until recently hindered their exploitation. Following comprehensive genomic and transcriptomic analysis of various diatom species, the biosynthetic mechanisms and regulation of the different branches of the pathway are now beginning to be elucidated. In this review, we provide a summary of the recent advances in understanding diatom isoprenoid synthesis and discuss the exploitation potential of diatoms as chassis for high-value isoprenoid synthesis.

Atomi, H., Reeve, J., 2019. Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon. Microbiology 165, 1166-1168.

https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000839

Thermococcus kodakarensis is a hyperthermophilic Euryarchaeon that grows well under laboratory conditions and, being naturally competent for genetic transformation, it has become a widely studied experimental model species. With the genome sequence available since 2004, combining genetic, enzymological and structural biochemical approaches has revealed previously unknown and unanticipated features of archaeal molecular biology and metabolism. T. kodakarensis DNA polymerase is already commercialized and with the details of metabolism and hydrogenase available, generating H2 from biopolymers solubilized at high temperatures, most notably chitin, now seems a very attractive possibility as a renewable energy bioprocess.

Avetisyan, K., Eckert, W., Findlay, A.J., Kamyshny, A., 2019. Diurnal variations in sulfur transformations at the chemocline of a stratified freshwater lake. Biogeochemistry 146, 83-100.

https://doi.org/10.1007/s10533-019-00601-5

In order to characterize biogeochemical sulfur cycling in the metalimnion of a thermally stratified freshwater lake, we followed changes in the concentrations and isotopic composition of sulfur species during a 24-h period, during which the chemocline oscillated at an amplitude of 5.3 m due to internal wave activity. Hourly sampling

at a fixed depth (17.1 m) enabled study of redox changes during the transition from oxic to sulfidic conditions and vice versa. The oxidation–reduction potential, pH, conductivity and turbidity correlated linearly with the water temperature (a proxy for depth relative to the chemocline). The highest concentrations of thiosulfate and sulfite were detected approximately 2.5 m below the chemocline. Concentrations of zero-valent sulfur increased ~ 10 fold when the chemocline rose into the photic zone due to phototrophic sulfide oxidation. Triple isotopic composition of sulfur species indicates a shift with depth from values typical for sulfate reduction right below the chemocline to values which may be explained by either sulfate reduction alone or by a combination of microbial sulfate reduction and microbial sulfate disproportionation. We conclude that consumption of hydrogen sulfide at the chemocline of Lake Kinneret is controlled by the combination of its chemical and/or chemotrophic oxidation to sulfur oxoanions and predominantly phototrophic oxidation to zero-valent sulfur.

Bachmann, R., Jilani, A., Ibrahim, H., Bahmann, D., Lang, C., Fischer, M., Bisping, B., Hackl, T., 2019. Signal pattern plot: a simple tool for time-dependent metabolomics studies by 1H NMR spectroscopy. Analytical and Bioanalytical Chemistry 411, 6857-6866.

https://doi.org/10.1007/s00216-019-02055-y

We show an alternative way to visualize time course NMR data without the application of multivariate data analysis, based on the temporal change of the metabolome of hazelnuts after mold infestation. Fresh hazelnuts were inoculated with eight different natural mold species and the growth was studied over a period of 14 days. The data were plotted in a color-coded scheme showing metabolic changes as a function of chemical shift, which we named signal pattern plot. This plot graphically displays alteration (trend) of a respected signal over time and allows visual interpretation in a simple manner. Changes are compared with a reference sample stored under identical conditions as the infected nuts. The plot allows, at a glance, the recognition of individual landmarks specific to a sample group as well as common features of the spectra. Each sample reveals an individual signal pattern. The plot facilitates the recognition of signals that belong to biological relevant metabolites. Betaine and five signals were identified that specifically changed upon mold infestation.

Baioumy, H., Lehmann, B., Ahmed Salim, A.M., Al-Kahtany, K., El-Sorogy, A., 2020. Geochemical characteristics of black shales from Triassic turbidites, Peninsular Malaysia: Implications for their origin and tectonic setting. Marine and Petroleum Geology 113, 104137.


Field observations indicate that shale intervals of Triassic turbidites from the Semanggol and Semantan formations in the Peninsular Malaysia occur as thick-bedded dark grey to black shales overlying conglomerate, pebbly sandstone, thick-bedded sandstone, and sandstone-shale interbeds. This sequence characterises a submarine fan depositional setting where the conglomerate, sand and sand/shale intercalations represent an inner and middle fan setting in a shallow marine environment, whereas the black shales were deposited in a deeper marine environment of the outer fan. The redox-sensitive trace-metal inventory (V, Ni, Cr) of the black shales is dominated by clastic input and the depositional environment is likely oxic/suboxic. TOC values are highly variable (3.2 ± 3.3 wt%) and derive from washed-in allochthonous organic material.

The Semantan Formation black shales have features of a felsic source rock, while black shales from the Semanggol Formation were inherited from more intermediate rocks as constrained by their Al2O3/TiO2 ratios. Similar Al2O3/SiO2 ratios as well as CIA values suggest wet paleoclimatic conditions and intensive weathering of source rocks during the Late Triassic deposition of both shales. The tectonic setting deduced from immobile-trace-metal ratios is a passive margin for the Semanggol black shales and a fore-arc-basin setting for the Semantan black shales. The inconsistency between the interpreted geological and geochemical tectonic settings, particularly for the Semanggol black shales, is due to the recycled nature of the sediment sources that were deposited in a different tectonic setting.

The clay fractions of both formations comprise of abundant illite and kaolinite, with some smectite in few samples from the Semantan Formation. Based on illite contents (38–68%) and IC values (0.45–0.62° Δ2θ), the studied black shales are in the late diagenesis stage. The organic matter in the Semanggol and Semantan black

shales is characterized by kerogen Type III proposing a terrestrial origin of the organic matter, which was transported along with the clastic sediments by turbidity currents.

Balcells, C., Foguet, C., Tarragó-Celada, J., de Atauri, P., Marin, S., Cascante, M., 2019. Tracing metabolic fluxes using mass spectrometry: Stable isotope-resolved metabolomics in health and disease. TrAC Trends in Analytical Chemistry 120, 115371.


Tracing metabolic fluxes, defined as the reaction and transport rates in living cells, is essential to characterize metabolic phenotypes. One of the most informative methods to predict fluxes is stable isotope-resolved metabolomics (SIRM). In SIRM, a biological system is fed with substrates labeled with stable heavy isotopes. This isotopic label propagates along metabolic pathways and is incorporated into metabolites. After incubation, metabolites are extracted, and the incorporation of the isotopic label is quantified with isotope-sensitive analytical techniques, either mass spectrometry (MS) or nuclear magnetic resonance (NMR). Here we review the most suitable and widely-used MS platforms and methodologies for SIRM. We also provide an overview of state of the art in the analysis of SIRM data to trace metabolic fluxes, covering both local flux predictions and network-wide flux analysis. Finally, we highlight the role of SIRM in shaping our current understanding of metabolism in both health and pathological conditions.

Bärenbold, F., Schmid, M., Brennwald, M.S., Kipfer, R., 2020. Missing atmospheric noble gases in a large, tropical lake: The case of Lake Kivu, East-Africa. Chemical Geology 532, 119374.


Lake Kivu is a 485 m deep tropical rift lake in East-Africa and well-known for its very high concentrations of dissolved carbon dioxide and methane in the stratified deep waters. In view of future large-scale methane extraction for power production, there is a need for predicting the evolution of gas concentrations and lake stability using numerical modelling. However, knowledge about the geochemical origin and transport processes affecting dissolved gases in the lake is still partially missing. Due to their inert nature, the analysis of dissolved noble gases can help to shed light on such questions. To learn more about transport processes in Lake Kivu, we extended a well-established sampling method for dissolved noble gases to work in the lake's high gas pressure waters. The results of our analysis show a distinct non-atmospheric isotopic signal in the deep waters (below ~250 m) with 3He/4He and 40Ar/36Ar ratios ~250% and ~20% higher than air saturated water (ASW). Moreover, the gas concentration profiles reveal a striking lack of atmospheric noble gases in the deep waters with respect to ASW. While Ne is depleted by ~45%, the more soluble 36Ar and Kr even decrease by ~70%. In contrast, 4He concentrations increase with depth by a factor of up to ~600. We attribute this excess He and the increases in 3He/4He and 40Ar/36Ar to the inflow of magmatic gases into Lake Kivu, along with a significant contribution of radiogenic 4He. To explain the depletion of atmospheric noble gases, we present and discuss three different scenarios, namely continuous outgassing, the inflow of depleted groundwater and a large past outgassing event. Due to the best agreement with our observations, we conclude that the inflow of depleted groundwater is likely responsible for the observed atmospheric noble gas depletions.


https://doi.org/10.1002/rcm.8511

Rationale: Stable isotopes of carbon and nitrogen have proved to be valuable tools for researchers working across the different subfields of ecology. However, the chemical pretreatment of samples prior to analytical determination of stable isotope ratios can influence the results, and therefore conclusions regarding the ecology of the taxon or system under study. Here, we determined the effect of vapor acidification with concentrated HCl

on the δ13C and δ15N values of particulate organic matter (POM), which are commonly used as baselines for studies of trophic ecology, or to understand oceanographic patterns.

Methods: Samples of marine POM were obtained along a large‐scale latitudinal gradient (ca 3000 km) along the Chilean coast, along with a range of oceanographic variables thought to potentially influence inorganic carbon at each sampling location. A random subset of 50 samples was divided into two parts: one acidified by HCl fumigation treatment, and the other acting as a control. We compared paired differences in δ13C and δ15N values measured by continuous flow isotope ratio mass spectrometry and used a model selection approach to examine which oceanographic factor best explained shifts in values following acid treatment.

Results: Acidification resulted in statistically significant reductions in both δ13C and δ15N values, but the effect was relatively small. The model that best explained the differences between acidified and non‐acidified δ13C values included depth, salinity and sea‐surface temperature at the sampling point. A regression of acidified on non‐acidified δ13C values shows that the treatment effect was strongest on samples more depleted in 13C.

Conclusions: The differences between δ13C and δ15N values in acidified and non‐acidified samples are linear and predictable. This implies that the nature of the POM and its possible alteration during the acid treatment are important factors that support the reliable determination of the values of δ13C and δ15N of POM.

Bassir, S.M., Madani, M., 2019. Predicting asphaltene precipitation during titration of diluted crude oil with paraffin using artificial neural network (ANN). Petroleum Science and Technology 37, 2397-2403.

https://doi.org/10.1080/10916466.2019.1570261

Asphaltene precipitation from crude oil in underground reservoirs and on ground facilities is one of the major problems in a large portion of oil production units around the world. Many scaling equations and intelligent predictive models using the artificial neural network (ANN) are proposed in the literature but none of them can be applied when crude oil is diluted with any types of paraffin. In this study, feed forward artificial neural network is used for prediction of the amount of asphaltene precipitated weight percent of diluted crude oil with paraffin based on titration tests data from published literature. Trial and error method is utilized to optimize the artificial neural network topology in order to enhance its strength of generalization. The results showed that there is good agreement between experimental and predicted values. This predictive model can be applied to estimate the amount of asphaltene precipitated weight percent when the crude oil is diluted with paraffin and to avoid experimental measurement that is time-consuming and requires expensive experimental apparatus as well as complicated interpretation procedure.

Bastidas-Oyanedel, J.-R., Schmidt, J.E., 2019. Biorefinery. Integrated Sustainable Processes for Biomass Conversion to Biomaterials, Biofuels, and Fertilizers, p. 763.

https://www.springer.com/gp/book/9783030109608

This book discusses the biorefinery of biomass feedstocks. In-depth chapters highlight the scientific and technical aspects and present a techno-economic analysis of such systems. By using a TEA approach, the authors present feasible pathways for conversion of biomass (both residual biomass, energy crops and algae biomass), showing the different possibilities for the production of biochemical materials, biofuels, and fertilizers. The concepts presented in this book will link companies, investors,

Presents a unique discussion of biomass conversion from a techno-economic perspective

Case-studies and examples are included to illustrate and demonstrate the methods presented in the book

Contains a framework to guide the process of investments, cost, and revenue of future biorefineries

Castilla-Archilla, Juan, O;Flaherty, Vincent, Lens, Piet N.L. Biorefineries: Industrial Innovation and Tendencies, Pages 3-35

Bentsen, Niclas Scott, Biomass for Biorefineries: Availability and Costs, Pages 37-48

Ashraf, Muhammad Tahir, Torres, Ana Inéz, Schmidt, Jens Ejbye, Stephanopoulous, George, Analysis and Optimization of Multi-actor Biorefineries, Pages 49-75

Puig-Arnavat, Maria, Thomsen, Tobias Pape, Ravenni, Giulia, Clausen, Lasse Røngaard, Sárossy, Zsuzsa, Ahrenfeldt, Jepser, Pyrolysis and Gasification of Lignocellulosic Biomass, Pages 79-110

Baldwin, Robert M. Upgrading Bio-oil: Catalysis and Refinery, Pages 111-151

Cybulska, Iwona, Chaturvedi, Tammy, Thomsen, Mett Hedegaard, Lignocellulosic Thermochemical Pretreatment Processes, Pages 153-165

Taher, Hanifa, Biodiesel: Use of Green Feedstocks and Catalysts, Pages 169-184

Wazeer, I., Hadi-Kali, K., AlNashef, I.M., Applications of Ionic Liquids and Deep Eutectic Solvents in Biorefinery-Biodiesel Production, Pages 185-210

Selvaraj, Munirasu, Banaat, Fawzi, Ethanol-Water Separation Using Membrane Technology, Pages 211-232

Caballero, Eduardo, Soto, Carmen, Valorization of Agro-Industrial Waste into Bioactive Compounds: Techno-Economic Considerations, Pages 235-252

Cecilia, Juan A., García-Sancho, Christina, Mairles-Torres, Pedro J., Luque, Rafael, Industrial Food Waste Valorization: A General Overview, Pages 253-277

Kádár, Zsófia, Fonseca, César, Bio-Products from Sugar-Based Fermentation Processes, Pages 281-312

Flotats, Xavier, Biogas: Perspectives of an Old Technology, Pages 313-349

Walling, Eric, Babin, Alexandre, Vaneeckhaute, Céline, Nutrient and Carbon Recovery from Organic Wastes, Pages 351-373

Bastidas-Oyanedel, Juan-Rodrigo, Bonk, Fabian, Thomsen, Mette Hedegaard, Schmidt, Jens Ejbye, The Future Perspectives of Dark Fermentation: Moving from Only Biohydrogen to Biochemicals, Pages 375-412

Sen, Biswarup, Aravind, J., Lin, Chiu-Yue, Lay, Chyi-How, Hsieh, Ping-Heng, Biohydrogen Production Perspectives from Organic Waste with Focus on Asia, Pages 413-435

Zhang, Fang, Zhen, Raymond Jianxiong, Anaerobic Thermophilic Mixed Culture Fermentation Processes, Pages 437-460

Bonk, Fabian, Bastidas-Oyanedel, Juan-Rodrigo, Yousef, Ahmed E., Schmidt, Jens Ejbye, Exploring the Selective Lactic Acid Production from Food Waste in Uncontrolled pH Mixed Culture Fermentations Using Different Reactor Configurations, Pages 461-477

Yousuf, Ahasa, Bastidas-Oyanedel, Juan-Rodrigo, Schmidt, Jens Ejbye, Effect of Total Solid Content and Pretreatment on the Production of Lactic Acid from Mixed Culture Dark Fermentation of Food Waste, Pages 479-490

Zeng, Raymond Jianxiong, Zhang, Fang, Use of Syngas for the Production of Organic Molecules by Fermentation, Pages 491-509

Moscoviz, Roman, Desmond-Le Quéméner, Elie, Trably, Eric, Bernet, Nicolas, Bioelectrochemical Systems for the Valorization of Organic Residues, Pages 511-534

Bastidas-Oyanedel, Juan-Rodrigo, Schmidt, Jens Ejbye, Techno-economic Analysis of Fermentation-Based Biorefinery: Creating Value from Food Residues, Pages 535-552

Pellis, Alessandro, Nyanhongo, Gibson S., Farmer, Thomas J.,, Recent Advances on Enzymatic Catalysis as a Powerful Tool for the Sustainable Synthesis of Bio-Based Polyesters, Pages 555-570

Guebitz, G. M., Pellis, Alessandro, Nyanhongo, Gibson S., Enzymatic Processing of Technical Lignins into Materials, Pages 571-592

Infelise, L., Kazimierczak, J., Wietecha, J. Kopania, E., GINEXTRA®: A Small-Scale Multipurpose Modular and Integrated Biorefinery Technology, Pages 593-614

Pratt, Steven, Vandi, Luigi-Jules, Gapes, Daniel, Werker, Alan, Oehmen, Adrian, Laycock, Bronwyn Polyhydroxyalkanoate (PHA) Bioplastics from Organic Waste, Pages 615-638

Bochenski, Tomasz, Chan, Wui Yar, Olsen, Bradley D. Schmidt, Jens Ejbye, Techno-economic Analysis for the Production of Novel Bio-derived Elastomers with Modified Algal Proteins as a Reinforcing Agent, Pages 639-654

Brown, J. Jed, Considerations for Producing Bioenergy from Halophyte Feedstocks, Pages 657-668

Almardeai, Saleha, Bastidas-Oyanedel, Juan-Rodrigo, Haris, Sabeera, Schmidt, Jens Ejbye, Characterization of Avicennia marina: An Arid-Coastal Biomass—Toward Biorefinery Products, Pages 669-677

AlMahri, Mariam Ali, Jung, Kichul, Alshehhi, Mashael, Almardeai, Saleha, Bastidas-Oyanedel, Juan-Rodrigo, Schmidt, Jens Ejbye, Techno-economic Assessment of Microalgae Biorefinery as a Source of Proteins, Pigments, and Fatty acids: A Case Study for the United Arab Emirates, Pages 679-693

Fang, Chuanji, Thomsen, Mette Hedegaard, Frankær, Bastidas-Oyanedel, Juan-Rodrigo, Brudecki, Grzegorz Przemyslaw, Schmidt, Jens Ejbye, Factors Affecting Seawater-Based Pretreatment of Lignocellulosic Date Palm Residues, Pages 695-713

Dzidzienyo, Prosper, Bastidas-Oyanedel, Juan-Rodrigo, Schmidt, Jens Ejbye, Pyrolysis Kinetics of Arid-Land Biomasses, Pages 715-725

Farzanah, Rashed H., Brudecki, Grzegorz Przemyslaw, Cybulska, Iwona, Bastidas-Oyanedel, Juan-Rodrigo, Brudecki, Schmidt, Jens Ejbye, F

Screening and Production of Biogas from Macro Algae Biomass of Padina boergesenii, Colpomenia sinuosa, and Ulva sp.Thomsen, Mette Hedegaard, Pages 727-740

Book Review:

Christi, Yusuf, Biorefinery: Integrated Sustainable Processes for Biomass Conversion to Biomaterials, Biofuels, and Fertilizers, J.-R. Bastidas-Oyanedel, J.E. Schmidt (Eds.), Springer, Cham, Switzerland (2019), (ISBN 978-3-030-10960-8 [xiv + 763 pp.]), Biotechnology Advances, 37(8), 107464 December 2019

With an all-encompassing title, this book on biorefineries covers a hodgepodge of topics. Conceptually, a biorefinery is akin to a petroleum refinery, producing diverse products from a biomass feedstock. A great diversity of physical, chemical and biological processes are used in converting a feedstock to desired products and feedstocks can be quite diverse, too. This diversity explains some of the hodgepodge, but not all. A second contributing factor appears to be the large number of authors (nearly 80) who have written the 33 chapters that comprise this book.

The chapters are grouped into seven parts. Part 1 has three chapters concerned with the preliminaries. Sustainability of production is supposedly the key logic behind using renewable biomass resources to produce goods and services, but several of the biorefinery case studies discussed in the first chapter fail on sustainability

score. A chapter examines the availability and cost of biomass for biorefineries. One chapter addresses the optimization problem of determining the most profitable sequence of processing technologies and products, given a biomass feedstock.

The three chapters in Part 2 focus on thermochemical processes. Discussed are pyrolysis and gasification of lignocellulosic biomass; catalytic upgrading and refining of biooil produced by pyrolysis of biomass; and thermochemical processes for pretreatment of lignocellulosic biomass. Part 3 has three chapters. Use of “green feedstocks” for biodiesel production is discussed, but many of the feedstocks mentioned are neither green nor practical. I doubt the practicality of making biodiesel from chicken fat, olive oil and sesame oil. A chapter suggests the use of ionic liquids and “deep eutectic” solvents for making biodiesel. These solvents are certainly not currently being used in commercial production of biodiesel and solvent-free transesterification of triglyceride oils with methanol, remains the established route for making biodiesel. The final chapter in this section deals with membrane-based separation of ethanol from water using pervaporation. Pervaporation is fine technically, but for economic reasons has failed to displace the combination of conventional distillation and molecular sieves in commercial production of fuel bioethanol.

The two chapters in Part 4, deal with the use of agroindustrial waste and food waste as production feedstock. Part 5 of the book is the longest and deals with products derived by fermentation of a feedstock. Sugar-based fermentation processes are devoted a chapter. Anaerobic digestion of organic waste to biogas, is discussed in one chapter. A chapter entitled “Nutrient and carbon recovery from organic wastes”, mostly repeats material covered in other areas of the book (thermochemical conversion, gasification, pyrolysis, anaerobic digestion, fermentation, etc.). A chapter deals with the potential of dark fermentation for producing products other than biohydrogen (mostly short-chain fatty acids). A separate chapter focuses on production of biohydrogen by dark fermentation of organic waste. Anaerobic dark fermentation for biogas and biohydrogen is further discussed in a chapter focusing on thermophilic mixed cultures. Two chapters deal with different aspects of production of lactic acid using food waste. Syngas, a mixture of carbon monoxide and hydrogen, produced from biomass via chemical processes, can be upgraded by microbial action, to chemicals such as ethanol and butanol. Syngas fermentation is devoted a chapter. Bioelectrochemical devices can be used to generate electricity and biochemicals from organic waste in processes involving microorganisms or isolated enzymes. A chapter is devoted to these systems. The final chapter in this section considers some economic aspects of fermentation-based biorefineries.

Part 6 focusses on bio-based polymers. The five chapters in this part deal with enzyme catalyzed production of polyesters; enzymatic processing of lignins to useful products; polyhydroxyalkanoate bioplastics from waste organics; technoeconomics of production of a bio-based elastomer; and a pilot biorefinery for producing biomaterials (mainly fiber) from the perineal shrub Spartium junceum (Spanish broom) native to the Mediterranean region.

Part 7 has six chapters focusing mostly on biomass derived from halophilic species that are salt-tolerant. A chapter is concerned with bioenergy from salt-tolerant higher plants. Currently, halophytes are barely used for bioenergy, but unsuccessful pilot scale operations have been attempted to make use of them. A chapter deals with possible bioenergy applications of lignocellulosic biomass of the only mangrove species native to coastal regions of United Arab Emirates. A chapter on technoeconomics of a microalgal biorefinery estimates a return on investment in excess of 38% with a payback period of under 3-years and an initial capital investment of around $138 million. Having worked with microalgae for many years, I find such assessments highly suspect. Many of the other technoeconomic assessments in this book are similarly questionable. A chapter deals with the use of seawater in hydrothermal pretreatment of date palm residues. The logic here is to save scarce freshwater by replacing it with seawater. After hydrothermal pretreatment, the biomass was washed with a lot of water (around ten times as much water by weight as the weight of the pretreated biomass) and this was apparently

freshwater. This must have nullified, or at least diminished, the intended saving of freshwater. A chapter considers the kinetics of pyrolysis of some lignocellulosic biomass (date palm and a halophyte). The final chapter concerns production of biogas from biomass of certain seaweeds (macroalgae).

There is some overlap among chapters and their quality varies. All chapters cite original literature and some are supported with illustrations in color. The book has a helpful 23-page subject index. It is available also as an e-book.

Bastrup, J., Birkelund, S., Asuni, A.A., Volbracht, C., Stensballe, A., 2019. Dual strategy for reduced signal-suppression effects in matrix-assisted laser desorption/ionization mass spectrometry imaging. Rapid Communications in Mass Spectrometry 33, 1711-1721.


Rationale: The molecular complexity of tissue features several signal‐suppression effects which reduce the ionization of analytes significantly and thereby weakens the quality of matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS) imaging (MALDI imaging). We report a novel approach in MALDI imaging by reducing signal‐suppression effects for the analysis of beta‐amyloid (Aβ) plaques, one pathological hallmark of Alzheimer's disease (AD).

Methods: We analyzed Aβ proteoforms from postmortem AD brains and brains from transgenic mice (APPPS1‐21) overexpressing familial AD mutations by combining two techniques: (1) laser capture microdissection (LCM) to accumulate Aβ plaques and (2) phosphoric acid (PA) as additive to the super‐2,5‐dihydroxybenzoic acid matrix.

Results: LCM and MALDI‐MS enabled tandem mass spectrometric fragmentation of stained Aβ plaques. PA improved the signal‐to‐noise (S/N) ratio, especially of the Aβ1‐42 peptide, by three‐fold compared with the standard matrix additive trifluoroacetic acid. The beneficial effect of the PA matrix additive in MALDI imaging was particularly important for AD brain tissue. We identified several significant differences in Aβ plaque composition from AD compared with APPPS1‐21, underlining the value of reducing signal‐suppressing effects in MALDI imaging.

Conclusions: We present a novel strategy for overcoming signal‐suppression effects in MALDI imaging of Aβ proteoforms.


https://www.frontiersin.org/article/10.3389/feart.2019.00297

Stability and mobility of organic matter in shale is significant from the perspective of carbon cycle. Shale can only be an effective sink provided that the organic carbon present is stable and immobile from the host sites and, not released easily during geological processes such as low pressure-temperature burial diagenesis and higher pressure-temperature subduction. To examine this, three Jurassic shale samples of known mineralogy and total organic carbon content, with dominantly continental source of organic matter, belonging to the Haynesville-Bossier Formation were combusted by incremental heating from temperature of 200 to 1400°C. The samples were analyzed for their carbon and nitrogen release profiles, bulk δ13C composition and C/N atomic ratio, based on which, at least four organic carbon components are identified associated with different minerals such as clay, carbonate, and silicate. They have different stability depending on their host sites and occurrences relative to the mineral phases and consequently, released at different temperature during combustion. The components identified are denoted as, C-1 (organic carbon occurring as free accumulates at the edge or mouth of pore spaces), C-2 (associated with clay minerals, adsorbed or as organomineral nanocomposites; with carbonate minerals, biomineralized and/or occluded), C-3(a) (occurring with silicate

minerals, biomineralized and/or occluded) and C-3(b) (graphitized carbon). They show an increasing stability and decreasing mobility from C-1 to C-3(b). Based on the stability of the different OC components, shale is clearly an efficient sink for the long term C cycle as, except for C-1 which forms a very small fraction of the total and is released at temperature of ∼200°C, OC can be efficiently locked in shale surviving conditions of burial diagenesis and, subduction at fore arc regions in absence of infiltrating fluids. Under low fluid flux, C-3(b) can be efficiently retained as a refractory phase in the mantle when subducted. It is evident that the association and interaction of the organic matter with the different minerals play an important role in its retention in the shale.

Bäurer, S., Ferri, M., Carotti, A., Neubauer, S., Sardella, R., Lämmerhofer, M., 2020. Mixed-mode chromatography characteristics of chiralpak ZWIX(+) and ZWIX(−) and elucidation of their chromatographic orthogonality for LC × LC application. Analytica Chimica Acta 1093, 168-179.


Two-dimensional liquid chromatography requires orthogonal columns and/or separation principles in the first and second separation dimension. It is sometimes not straightforward to achieve. Chiral columns could expand the toolbox for 2D-LC, but are rarely exploited for this purpose, not least due to missing understanding of retention principles under non-chiral application conditions. To gain more insight, in this study Chiralpak ZWIX(+) and ZWIX(−), based on zwitterionic quinine and quinidine carbamate selectors, were carefully characterized by molecular dynamics simulations, lipophilicity/hydrophilicity measurements of selectors, pH-dependent ζ-potential determinations, and chromatographic characterization in RPLC and HILIC modes combined with unsupervised principal component analysis to extract classification of these columns in comparison to a number of commercial benchmarks (RP, HILIC and mixed-mode columns). The results showed that these chiral columns can be classified as mixed-mode chromatography phases with balanced lipophilic-hydrophilic surface character, excess of negative net charge due to sulfonic acid groups (in spite of weakly basic quinuclidine and quinoline rings), and multimodal applicability (RP, HILIC and polar organic elution modes). Orthogonality mapping in comparison to a number of modern HILIC and mixed-mode columns revealed that Poroshell HILIC-Z (with a zwitterionic ligand on 2.7 μm core-shell particles) can be beneficially combined as second dimension with the ZWIX column for comprehensive LC × LC. The online hyphenation of this 2D-LC system with complementary detection modalities including UV (DAD for chromophoric substances), charged aerosol detection (for universal detection and calibration of non-volatile analytes) and high-resolution mass spectrometry (ESI-QTOF-MS/MS for identification) provided an advanced method for comprehensive impurity profiling, applicable for instance for amino acid pharmaceutical products.

Becerra-Valdivia, L., Leal-Cervantes, R., Wood, R., Higham, T., 2020. Challenges in sample processing within radiocarbon dating and their impact in 14C-dates-as-data studies. Journal of Archaeological Science 113, 105043.


For decades, researchers have employed sets of radiocarbon dates to reconstruct trends in ancient human populations. The overarching assumption in this analysis is that the frequency of dates is proportional to the magnitude of past human activity. Thus, the distribution of summed or otherwise summarized dates is used to extrapolate population density and mobility patterns. There are, however, a number of underlying assumptions associated with this analysis that workers address to varying degrees and which, if false and not critically accounted for, will introduce bias, misrepresent the magnitude of activity, and ultimately prove misleading in archaeological interpretations. In this regard, research has so far mainly focused on correcting for the effects of time-dependent degradation of archaeological sites and constituent materials, calibration irregularities, and the efficacy of the statistical methods used. Assumptions directly related to sample processing in radiocarbon dating, however, are less discussed in ‘14C-dates-as-data’ analyses. It is, for example, assumed that all carbonaceous materials will yield sufficient, endogenous carbon for radiocarbon measurement. Yet sample failure in radiocarbon dating is common and contingent on, largely, deterministic factors such as post-depositional environment. Sets of radiocarbon dates analyzed, therefore, represent successful measurements

independent of reliability. In this work, we discuss the biases introduced by challenges in radiocarbon processing and their impact on 14C-dates-as-data studies.

Beeler, S.R., Gomez, F.J., Bradley, A.S., 2020. Controls of extreme isotopic enrichment in modern microbialites and associated abiogenic carbonates. Geochimica et Cosmochimica Acta 269, 136-149.


Microbialites and abiogenic carbonates of the closed-basin hypersaline lake Laguna Negra (Catamarca Province, Argentina) are highly enriched in both 13C and 18O. These carbonates precipitate in the zone of recharge where lake water mixes with groundwater. We examined the processes controlling the isotopic evolution of input waters in order to better interpret the isotopic compositions of the carbonates. Large enrichments of 13C in dissolved inorganic carbon and 18O in water occur as input groundwater chemically evolves. These enrichments can be explained through the abiotic processes of water-equilibration, evaporation, degassing, and carbonate precipitation. The 13C and 18O contents of lake carbonates are consistent with equilibrium precipitation from lake water indicating that the currently ongoing processes can explain the isotopic patterns observed in carbonates. Isotopic compositions of these microbialites are largely unrelated to the biological processes controlling microbialite formation – a pattern that may be generalizable to other settings. However, the isotopic compositions of these microbialites record information about their depositional environment.

Beisbart, C., 2019. (Trans-)planetary sustainability once more – a reply to Losch. International Journal of Astrobiology 18, 590-591.

https://doi.org/10.1017/S1473550419000028

In this reply to Losch (2019), I show that, Losch's own judgement notwithstanding, his plea for a concept of (trans-)planetary sustainability does propose conceptual change. I further argue that he has not provided convincing reasons to think that the label ‘planetary’ is superior to ‘trans-planetary’. I summarize my concerns about the plea for introducing the notion of (trans-)planetary sustainability and a related ethics.

Original Article: Beisbart, C (2019) Is trans-planetary sustainability a good idea? – An answer from the perspective of conceptual engineering. International Journal of Astrobiology. https://doi.org/10.1017/S1473550418000472

Comment: Losch, A., 2019. Planetary sustainability: transitions of an idea. International Journal of Astrobiology 18, 592-594.

Belhaj, A.F., Elraies, K.A., Janjuhah, H.T., Tasfy, S.F.H., Yahya, N., Abdullah, B., Umar, A.A., Ghanem, O.B., Alnarabiji, M.S., 2019. Electromagnetic waves-induced hydrophobic multiwalled carbon nanotubes for enhanced oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2667-2670.

https://doi.org/10.1007/s13202-019-0653-6

Extracting the trapped oil into the pores is still a massive challenging. In this work, multiwalled carbon nanotubes were utilized to investigate the influence of the nanofluid’s flow rate on the oil recovery in enhanced oil recovery (EOR) stage. At the optimum conditions, comparative study was conducted to figure out the impact of EM waves on the recovery efficiency. The experimental study proved that 2 mL/min is the optimum flow rate for the utilized fluid. EM waves could enhance the recovered oil in EOR stage by 24.5% ROIP. The increment was ascribed to the extraordinary role of EM waves in increasing the viscosity of the nanofluid.


https://doi.org/10.1038/s41559-019-1005-0

Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S ribosomal RNA gene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol–Danakil area in Ethiopia. We identified two physicochemical barriers to life in the presence of surface liquid water defined by (1) high chaotropicity–low water activity in Mg2+/Ca2+-dominated brines and (2) hyperacidity–salt combinations (pH ~0/NaCl-dominated salt saturation). When detected, life was dominated by highly diverse ultrasmall archaea that were widely distributed across phyla with and without previously known halophilic members. We hypothesize that a high cytoplasmic K+-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during several transitions to extreme halophily. We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond.



Shewanella is a genus of marine bacteria capable of dissimilatory iron reduction (DIR). In the context of deep-sea mining activities or submarine mine tailings disposal, dissimilatory iron reducing bacteria may play an important role in biogeochemical reactions concerning iron oxides placed on the sea bed. In this study, batch experiments were performed to evaluate the capacity of Shewanella loihica PV-4 to bioreduce different iron oxides (ferrihydrite, magnetite, goethite and hematite) under conditions similar to those in anaerobic sea sediments. Results showed that bioreduction of structural Fe(III) via oxidation of labile organic matter occurred in all these iron oxides. Based on the aqueous Fe (II) released, derived Fe(II)/acetate ratios and bioreduction coefficients seem to be only up to about 4% of the theoretical ones, considering the ideal stoichiometry of the reaction. A loss of aqueous Fe (II) was caused by adsorption and mineral transformation processes. Scanning electron microscope images showed that Shewanella lohica was attached to the Fe(III)-oxide surfaces during bioreduction. Our findings suggest that DIR of Fe(III) oxides from mine waste placed in marine environments could result in adverse ecological impacts such as liberation of trace metals in the environment.



Surface ecosystems are rapidly changing on a global scale and it is important to understand how this influences aquifers in the subsurface, as groundwater quality is a major concern for future generations. Dissolved organic matter (DOM) contains molecular and isotopic signals from surface-derived inputs as well as from the biotic and abiotic subsurface environment and is therefore ideal to study the connectivity between both environments. We evaluated a 3-year time series of DOM composition using ultrahigh resolution mass spectrometry and age using 14C accelerator mass spectrometry along a hillslope well transect in the fractured bedrock of the Hainich Critical Zone Exploratory, Germany. We found a wide range of DOM 14C depletion, from Δ14C = −47.9 to Δ14C = −782.4, within different zones of the shallow groundwater. The 14C content of DOM mirrored the connectivity of the aquifers to the surface. The composition of DOM was highly interrelated with its 14C age. The proportions of surface-derived DOM components decreased with DOM age, whereas microorganism-derived

DOM components increased. The intensity of surface-sourced DOM signals differed between the wells and likely reflected the hydrological complexity of fractured-rock environments. During recharge, DOM was more enriched in Δ14C, contained more surface-derived molecular components and was more diverse. As a potential response to the varying DOM substrate, bacterial 16S rRNA gene analysis revealed community evolution and increased bacterial diversity during recharge. The influx of diverse, surface-derived DOM potentially fueled evolution within the autochthonous bacterial communities, as in contrast to DOM, the bacterial community did not retreat to the initial diversity and community composition during the recession period. Our results demonstrate on the one hand that combined analyses of the composition and age of groundwater DOM strongly contribute to the understanding of interconnections, community evolution and the functioning of subsurface ecosystems and on the other hand that changes in surface ecosystems have an imprint on subsurface ecosystems.



The Paluxy formation is being considered as a prospective CO2 reservoir at the Kemper County CO2 Storage Complex. Here, the pore and pore-throat size distributions and connectivity of the Paluxy formation is evaluated through analysis of 3D X-ray Computed Tomography images. In spite of resolution limitations that constrain the pore-throat sizes detectable by imaging, the permeability contributing pore-throats are successfully characterized through 3D imaging analysis. Image-obtained pore and pore-throat size distributions and pore connectivity are then utilized to construct pore network models and simulate permeability. After CO2 is injected, it will dissolve into formation brine and create conditions favorable for dissolution of primary minerals and precipitation of secondary minerals. These reactions will alter the porosity and permeability of the system to varying degrees depending on the spatial location of reactions. Here, the possible porosity-permeability evolution is simulated using pore network models considering mineral reactions occurring uniformly and non-uniformly throughout the network. For a given change in porosity, there is a large range of possible permeability outcomes. Depending on the extent and spatial location of mineral reactions, permeability may decrease by more than one order of magnitude as minerals precipitate. During dissolution, simulated permeability increases as much as 500%.

Bergk Pinto, B., Maccario, L., Dommergue, A., Vogel, T.M., Larose, C., 2019. Do organic substrates drive microbial community interactions in Arctic snow? Frontiers in Microbiology 10, 2492. doi: 10.3389/fmicb.2019.02492.

https://www.frontiersin.org/article/10.3389/fmicb.2019.02492

The effect of nutrients on microbial interactions, including competition and collaboration, has mainly been studied in laboratories, but their potential application to complex ecosystems is unknown. Here, we examined the effect of changes in organic acids among other parameters on snow microbial communities in situ over 2 months. We compared snow bacterial communities from a low organic acid content period to that from a higher organic acid period. We hypothesized that an increase in organic acids would shift the dominant microbial interaction from collaboration to competition. To evaluate microbial interactions, we built taxonomic co-variance networks from OTUs obtained from 16S rRNA gene sequencing. In addition, we tracked marker genes of microbial cooperation (plasmid backbone genes) and competition (antibiotic resistance genes) across both sampling periods in metagenomes and metatranscriptomes. Our results showed a decrease in the average connectivity of the network during late spring compared to the early spring that we interpreted as a decrease of cooperation. This observation was strengthened by the significantly more abundant plasmid backbone genes in the metagenomes from the early spring. The modularity of the network from the late spring was also found to be higher than the one from the early spring, which is another possible indicator of increased competition. Antibiotic resistance genes were significantly more abundant in the late spring metagenomes. In addition, antibiotic resistance genes were also positively correlated to the organic acid concentration of the snow across

both seasons. Snow organic acid content might be responsible for this change in bacterial interactions in the Arctic snow community.

Bhattacharya, R., Osburn, C.L., 2020. Spatial patterns in dissolved organic matter composition controlled by watershed characteristics in a coastal river network: The Neuse River Basin, USA. Water Research 169, 115248.


The effect of watershed characteristics (land use land cover and morphology) on spatial variability in dissolved organic matter (DOM) composition, and concentrations of dissolved organic carbon [DOC] and nitrogen [DON] was assessed in a coastal river basin draining into Pamlico Sound in eastern North Carolina, USA. Understanding the factors that influence DOM concentration and composition i.e., structurally complex molecules with high molecular weight versus low molecular weight, simple molecules can provide insights on DOM cycling and water composition implications. Such information is imperative for large coastal river networks undergoing rapid and intense land use and land cover (LULC) changes. DOM composition was estimated using optical indices calculated from DOM absorbance and fluorescence measurements. DOM was derived from terrestrial sources, and ordination analysis indicated that LULC, in particular, % wetland area was the most significant control on DOM composition and concentration. Wetland and agricultural coastal streams were abundant in humic and complex DOM, whereas forested and urban streams were least abundant in humic DOM. We speculate that greater availability of mobilizable DOM in wetland and agricultural watersheds contributed to this observation. In comparison, mixed urbanized and forested streams in North Carolina’s Piedmont region were abundant in [DOC], less complex, low molecular weight DOM, as well as greater amounts [DON] due to higher urban runoff and elevated DOM production in these streams. Our results indicated that physiographic transition from Piedmont to coastal plain and varying LULC influenced the spatial variability in DOM composition and concentration. Our findings highlight that increasing anthropogenic alterations might increase the abundance of reactive DOM in coastal rivers and estuaries resulting in severe water quality issues. This information is important for monitoring and developing land use policies.

Bhowmik, S., Krishnamurthy, R., 2019. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nature Chemistry 11, 1009-1018.

https://doi.org/10.1038/s41557-019-0322-x

Hypotheses of the origins of RNA and DNA are generally centred on the prebiotic synthesis of a pristine system (pre-RNA or RNA), which gives rise to its descendent. However, a lack of specificity in the synthesis of genetic polymers would probably result in chimeric sequences; the roles and fate of such sequences are unknown. Here, we show that chimeras, exemplified by mixed threose nucleic acid (TNA)–RNA and RNA–DNA oligonucleotides, preferentially bind to, and act as templates for, homogeneous TNA, RNA and DNA ligands. The chimeric templates can act as a catalyst that mediates the ligation of oligomers to give homogeneous backbone sequences, and the regeneration of the chimeric templates potentiates a scenario for a possible cross-catalytic cycle with amplification. This process provides a proof-of-principle demonstration of a heterogeneity-to-homogeneity scenario and also gives credence to the idea that DNA could appear concurrently with RNA, instead of being its later descendent.

Bian, J., Olesik, S.V., 2020. Polyvinylpyrrolidone composite nanofibers as efficient substrates for surface-assisted laser desorption/ionization mass spectrometry. International Journal of Mass Spectrometry 448, 116253.


A matrix-free laser desorption/ionization mass spectrometry (LDI-MS) approach was developed using electrospun composite nanofibers with controllable size, morphology and composition. Composite polyvinylpyrrolidone (PVP) nanofibers with added nanoparticles to enhance the absorption of laser energy absorber were studied. Fractal dimensional analysis was conducted to evaluate the electrospinning process for

the first time, which provided useful information on the repeatability of nanofiber production. The performance of the nanofiber-assisted laser desorption/ionization method was investigated through characterization of small drug molecules and synthetic oligomers. Homogeneous sample distribution was achieved by eliminating the “sweet spot”, resulting in good reproducibility. Mass spectra features clean background, that is especially beneficial for interpretation of small molecules. High sensitivity for small drug molecules and synthetic oligomers was obtained with limits of detection limits down to the low attomolar range. The combination of composite nanofibers with LDI-MS is a versatile and sensitive approach for detection and characterization of analytes with broad range of molecular weight.


https://doi.org/10.1007/s12010-019-03058-2

Bioremediation has been attracting researchers’ attention to develop as a technique to remove the pollution of crude oil in the environment. However, more or stronger novel strains capable of crude oil removal are still required. In this study, the potential of five newly isolated bacterial strains for crude oil abatement was evaluated in the liquid medium and contaminated soil individually and as a mixed consortium. Raoultella ornithinolytica strain PS exhibited the highest ability and degraded up to 83.5% of crude oil. Whereas Bacillus subtilis strain BJ11 degraded 81.1%, Acinetobacter lwoffii strain BJ10 degraded 75.8%, Acinetobacter pittii strain BJ6 degraded 74.9%, and Serratia marcescens strain PL degraded only 70.0% of crude oil in the liquid media. The consortium comprising the above five strains degraded more than 94.0% of crude oil after 10 days of incubation in the liquid medium. The consortium degraded more than 65.0% of crude oil after 40 days incubation even in the contaminated soil. The five crude oil degrading strains, especially their consortium, exhibited a high capability to break down a wide range of compounds in crude oil including straight-chain alkanes, branched alkanes, and aromatic hydrocarbons. These strains, especially as consortia, have good potential of application in the remediation of crude oil–contaminated environments.

Blattmann, T.M., Liu, Z., Zhang, Y., Zhao, Y., Haghipour, N., Montluçon, D.B., Plötze, M., Eglinton, T.I., 2019. Mineralogical control on the fate of continentally derived organic matter in the ocean. Science 366, 742-745.


Abstract: First-order relationships between organic matter content and mineral surface area have been widely reported and are implicated in stabilization and long-term preservation of organic matter. However, the nature and stability of organomineral interactions and their connection with mineralogical composition have remained uncertain. In this study, we find that continentally derived organic matter of pedogenic origin is stripped from smectite mineral surfaces upon discharge, dispersal, and sedimentation in distal ocean settings. In contrast, organic matter sourced from ancient rocks that is tightly associated with mica and chlorite endures in the marine realm. These results imply that the persistence of continentally derived organic matter in ocean sediments is controlled to a first order by phyllosilicate mineralogy.

Edioptr's summary: Bound to rock. Organic matter binds to phyllosilicates, a process which affects both its transport and chemical stability. How does that affect the fate of terrestrial organic carbon that enters the ocean? Blattmann et al. show that organic carbon derived from soils is stripped from mineral surfaces upon discharge and dispersal into the ocean, whereas organic matter derived from ancient rocks is preserved there. Their results show that preservation of continentally derived organic matter in marine sediments is controlled largely by phyllosilicate mineralogy.

Boatman, E.M., Goodwin, M.B., Holman, H.-Y.N., Fakra, S., Zheng, W., Gronsky, R., Schweitzer, M.H., 2019. Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex. Scientific Reports 9, 15678.

https://doi.org/10.1038/s41598-019-51680-1

The idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.

Böhme, M., Spassov, N., Fuss, J., Tröscher, A., Deane, A.S., Prieto, J., Kirscher, U., Lechner, T., Begun, D.R., 2019. A new Miocene ape and locomotion in the ancestor of great apes and humans. Nature 575, 489-493.

https://doi.org/10.1038/s41586-019-1731-0

Many ideas have been proposed to explain the origin of bipedalism in hominins and suspension in great apes (hominids); however, fossil evidence has been lacking. It has been suggested that bipedalism in hominins evolved from an ancestor that was a palmigrade quadruped (which would have moved similarly to living monkeys), or from a more suspensory quadruped (most similar to extant chimpanzees). Here we describe the fossil ape Danuvius guggenmosi (from the Allgäu region of Bavaria) for which complete limb bones are preserved, which provides evidence of a newly identified form of positional behaviour—extended limb clambering. The 11.62-million-year-old Danuvius is a great ape that is dentally most similar to Dryopithecus and other European late Miocene apes. With a broad thorax, long lumbar spine and extended hips and knees, as in bipeds, and elongated and fully extended forelimbs, as in all apes (hominoids), Danuvius combines the adaptations of bipeds and suspensory apes, and provides a model for the common ancestor of great apes and humans.

Bonan, G.B., Lombardozzi, D.L., Wieder, W.R., Oleson, K.W., Lawrence, D.M., Hoffman, F.M., Collier, N., 2019. Model structure and climate data uncertainty in historical simulations of the terrestrial carbon cycle (1850–2014). Global Biogeochemical Cycles 33, 1310-1326.

https://doi.org/10.1029/2019GB006175

The divergence among Earth system models in the terrestrial carbon cycle has prompted interest in how to reduce uncertainty. Previous studies have identified model structural uncertainty arising from process parameterizations and parameter values. The current study highlights the importance of climate forcing in generating carbon cycle uncertainty. We use simulations in which three models (Community Land Model version 4 (CLM4), CLM4.5, CLM5) with substantially different carbon cycles are forced with two climate reconstructions (CRUNCEPv7, Global Soil Wetness Project 3 version 1 (GSWP3v1)) to examine the contributions of model structure and climate to uncertainty in the carbon cycle over the period 1850–2014. Climate uncertainty for global annual net biome production exceeds one third of total uncertainty (defined as the sum of climate and model structure uncertainty) in the first half of the twentieth century, but declines after the 1950s. Global annual gross primary productivity, net primary productivity, heterotrophic respiration, and vegetation and soil carbon stocks have substantial climate uncertainty (relative to total uncertainty) throughout the simulation period. Climate forcing contributes more than one half of total uncertainty for these carbon cycle fluxes and stocks throughout boreal North America and Eurasia, some midlatitude regions, and in eastern Amazonia and western equatorial Africa during the decade 2000–2009. Comparison with observationally based data sets of the carbon cycle using model benchmarking methods provides insight into strengths and deficiencies among models and climate forcings, but we caution against overreliance on benchmarking to

discriminate among models. The conceptualization of uncertainty arising from this study implies embracing multiple feasible model simulations rather than focusing on which model or simulation is best.

Bonner, R., Hopfgartner, G., 2019. SWATH data independent acquisition mass spectrometry for metabolomics. TrAC Trends in Analytical Chemistry 120, 115278.


Systems Biology and ‘Omics’ require reproducible identification and quantitation of many compounds, preferably in large sample cohorts. Liquid chromatography-mass spectrometry is important since data generated can be used for structure elucidation and highly specific targeted quantitation. Despite great success, the technique has limitations such as: compound coverage in one analysis, method development time and single sample analysis time which determines throughput. New instrument capabilities have led to improved methods, including ‘Data Independent Acquisition’ so-called because acquisition is not changed by acquired data. SWATH-MS is a specific example that has quickly become prominent in proteomics because of increased peptide coverage, high quantitation accuracy, excellent reproducibility and the generation of a ‘digital map’. These capabilities are important in small molecules analyses although uptake in these applications has been slower. We describe the SWATH-MS technique, review its use in applications such as metabolomics and forensics, and summarize on-going improvements and future prospects.

Borrego-Varillas, R., Nenov, A., Ganzer, L., Oriana, A., Manzoni, C., Tolomelli, A., Rivalta, I., Mukamel, S., Garavelli, M., Cerullo, G., 2019. Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules. Chemical Science 10, 9907-9921.

http://dx.doi.org/10.1039/C9SC03871J

Two-dimensional (2D) spectroscopy, originally developed for nuclear magnetic resonance, has been recently extended to the infrared and visible regimes. In this technique sequences of femtosecond light pulses are used to interrogate molecular systems and show, by a double Fourier transform, the correlation between excitation and detection frequencies. Extension to the ultraviolet (UV) regime is of great interest and promises to deliver rich structural and dynamical information on biomolecules such as DNA and proteins; however, it must overcome significant technical challenges. This review summarizes the current development status of 2DUV spectroscopy. After discussing the scientific case for the technique, we introduce its basic principles and review its experimental implementations, as well as the computational tools that have been developed to model the experiments. We conclude by giving a few application examples, which highlight the potential of 2DUV spectroscopy and motivate its further development.

Boswell, R., Myshakin, E., Moridis, G., Konno, Y., Collett, T.S., Reagan, M., Ajayi, T., Seol, Y., 2019. India National Gas Hydrate Program Expedition 02 summary of scientific results: Numerical simulation of reservoir response to depressurization. Marine and Petroleum Geology 108, 154-166.


The India National Gas Hydrate Program Expedition 02 (NGHP-02) discovered gas hydrate at high saturation in sand reservoirs at several sites in the deepwater Bay of Bengal. To assess the potential response of those deposits to scientific depressurization experiments, comprehensive geologic models were constructed to enable numerical simulation for two sites. Both sites (NGHP-02-09 and NGHP-02-16) feature thick sequences of thinly-interbedded reservoir and non-reservoir facies at sub-seafloor depths less than 300 m and sub-sea depths of 2400 m or more. These settings pose significant challenges to current modeling capabilities. First, the thinly-interbedded reservoir architecture complicates the determination of basic reservoir parameters from both log and core data due to measurement resolution issues. Secondly, the fine scale variation in sediment properties imparts great contrasts in key parameters over very short distances, creating high gradients at multiple scales and varying orientations that necessitate careful design of high-definition simulation grids. Thirdly, the deposits include internal sources of water, as well as a range of complex boundary conditions, including variable

permeability within the overlying mud-rich “seals,” that complicate reservoir depressurization. Lastly, because of the unique combination of great water depth and relatively shallow sub-seafloor depth: models designed to maximize the dissociation rate impose large pressure drawdowns on relatively low-strength sediments. This condition renders the proper evaluation and integration of the geomechanical response to hydrate dissociation critical. In this report, we review the history of gas hydrate reservoir simulation, discuss methods for creating geologic input models, and summarize the key findings and implications of the collaborative NGHP-02 numerical simulation effort. Together, the studies confirm the viability of the modeled accumulations for scientific testing and identify key challenges related to the selection of specific test sites and the design of test wells.

Boswell, R., Yoneda, J., Waite, W.F., 2019. India National Gas Hydrate Program Expedition 02 summary of scientific results: Evaluation of natural gas-hydrate-bearing pressure cores. Marine and Petroleum Geology 108, 143-153.


India's National Gas Hydrate Program (NGHP) Expedition-02 was conducted in 2015 with the goal of investigating numerous locations that had been determined to be prospective for gas hydrate at high saturation in sand-rich reservoirs. Initial logging while drilling data revealed extensive sand-rich gas hydrate occurrences at multiple drill sites in two broad areas. These sites were further investigated through the acquisition and analyses of pressure cores designed to document 1) gas hydrate occurrence within the reservoirs; 2) the petrophysical nature of the reservoir and associated seals, in their native state as well as during and after the dissociation of gas hydrate; 3) the geomechanical nature of the reservoir and seals; and 4) the geochemical nature of reservoir fluids. The cores were initially evaluated at sea, and select subsamples were transferred for more extensive analyses at specialized laboratories both in Japan and in the United States. The samples encompassed a wide range of gas hydrate saturation (from 0 to 100%) within reservoir sediments ranging from sandy silts to gravels, providing opportunities to extend and refine insights into the nature of gas hydrate reservoirs gained in previous programs. Select findings and implications of this coordinated pressure-core evaluation program are reported in numerous papers within the NGHP-02 Special Thematic Volume and are summarized here with respect to the following issues: the evaluation and mitigation of core disturbance, the assessment of gas hydrate occurrence and saturation, the geomechanics and petrophysics of both reservoirs and “seals” in situ, and the potential dynamic geomechanical and petrophysical behavior of reservoir and seals during production.


http://dx.doi.org/10.1039/C9AY01859J

The detection of asphaltic petroleum by surface enhanced Raman scattering (SERS) is uncomplicated, except in instances where the petroleum has been mixed with other components that also exhibit a strong Raman effect. Such a situation is common where, for example, petroleum is mixed with other naturally occurring materials in sedimentary environments. Sedimentary organic matter in deserts, on beaches, on continental shelves and in the deep sea may contain a variety of compound types that includes pigments and humic compounds, all of which are also amenable to surface enhanced Raman scattering, making the detection of asphaltic petroleum by SERS in these natural environments complicated. However, for a beach-sediment comprising sediment weathered from exhumed petroleum reservoirs and source rocks (naturally occurring sources of petroleum) it can be shown that the asphaltic component of a surface enhanced Raman spectra can be found by deconvolving asphaltene, humic acid and pigments using entire spectra. This is achieved by finding matches on look-up tables comprising entire spectra with varied contributions from different compounds. In using the entire spectra, subjectivity introduced by fitting individual curves to match multiple Raman bands is reduced, minimising the consequences of what can otherwise be a process that involves arbitrary decision making. Using this approach it can be shown that a SERS-assay of asphaltic materials in sediments from a foreshore in Northern Scotland can

produce results that benchmark reasonably against standard methods, and data that yields interpretations of the natural environment that are consistent with that derived from comparator GC-MS data.

Bowles, M.W., Samarkin, V.A., Hunter, K.S., Finke, N., Teske, A.P., Girguis, P.R., Joye, S.B., 2019. Remarkable capacity for anaerobic oxidation of methane at high methane concentration. Geophysical Research Letters 46, 12192-12201.

https://doi.org/10.1029/2019GL084375

Anaerobic oxidation of methane (AOM), a central process in the carbon cycle of anoxic environments, moderates the release of methane from soils and sediments to water bodies and, ultimately, the atmosphere. The regulation of AOM in the environment remains poorly constrained. Here we quantified AOM and sulfate reduction (SR) rates in diverse deep seafloor samples at in situ pressure and methane concentration and discovered that, in some cases, AOM exceeded SR rates by more than four times when methane concentrations were above 5 mM. Methane concentration also affected other carbon-cycling processes (e.g., carbon assimilation) in addition to SR. These results illustrate that substantial amounts of methane may be oxidized independent of SR under in situ conditions, reshaping our view of the capacity and mechanism of AOM in methane-rich environments, including the deep biosphere, where sulfate availability is considered to limit AOM.



There are numerous reports demonstrating the heterogeneous spatial distributions of lipids throughout biology using mass spectrometry imaging (MSI). However, despite these and the biological significance of lipid alterations there remains a surprising lack of understanding regarding the underlying origins of the spatial distributions detected with MSI. With the rapid improvements in analytical capabilities of MSI instrumentation, it is now at the point that these biological questions can begin to be addressed. In this review we focus on (i) work providing insight into the biochemical origins of lipid spatial distributions, with an emphasis on the role of localised enzymatic processes in determining lipid compositions; (ii) use of stable isotope labelling to spatially-resolve the kinetics of lipid synthesis; and (iii) current challenges faced by the lipid MSI community and new analytical methods to overcome them. Combined, these topics highlight the added biological information that can be acquired from the MSI of lipids.

Braga, R., Iglesias, R.S., Romio, C., Praeg, D., Miller, D.J., Viana, A., Ketzer, J.M., 2020. Modelling methane hydrate stability changes and gas release due to seasonal oscillations in bottom water temperatures on the Rio Grande cone, offshore southern Brazil. Marine and Petroleum Geology 112, 104071.


The stability of methane hydrates on continental margins worldwide is sensitive to changes in temperature and pressure conditions. It has been shown how gradual increases in bottom water temperatures due to ocean warming over post-glacial timescales can destabilize shallow oceanic hydrate deposits, causing their dissociation and gas release into the ocean. However, bottom water temperatures (BWT) may also vary significantly over much shorter timescales, including due to seasonal temperature oscillations of the ocean bottom currents. In this study, we investigate how a shallow methane hydrate deposit responds to seasonal BWT oscillations with an amplitude of up to 1.5 °C. We use the TOUGH + HYDRATE code to model changes in the methane hydrate stability zone (MHSZ) using data from the Rio Grande Cone, in the South Atlantic Ocean off the Brazilian coast. In all the cases studied, BWT oscillations resulted in significant gaseous methane fluxes into the ocean for up to 10 years, followed by a short period of small fluxes of gaseous methane into the ocean, until they stopped completely. On the other hand, aqueous methane was released into the ocean during the 100 years simulated, for all the cases studied. During the temperature oscillations, the MHSZ recedes continuously both

horizontally and, in a smaller scale, vertically, until a permanent and a seasonal region in MHSZ are defined. Sensitivity tests were carried out for parameters of porosity, thermal conductivity and initial hydrate saturation, which were shown to play an important role on the volume of methane released into the ocean and on the time interval in which such release occurs. Overall, the results indicate that in a system with no gas recharge from the bottom, seasonal temperature oscillations alone cannot account for long-term gas release into the ocean.

Brittingham, A., Hren, M.T., Hartman, G., Wilkinson, K.N., Mallol, C., Gasparyan, B., Adler, D.S., 2019. Geochemical evidence for the control of fire by Middle Palaeolithic hominins. Scientific Reports 9, 15368.

https://doi.org/10.1038/s41598-019-51433-0

The use of fire played an important role in the social and technological development of the genus Homo. Most archaeologists agree that this was a multi-stage process, beginning with the exploitation of natural fires and ending with the ability to create fire from scratch. Some have argued that in the Middle Palaeolithic (MP) hominin fire use was limited by the availability of fire in the landscape. Here, we present a record of the abundance of polycyclic aromatic hydrocarbons (PAHs), organic compounds that are produced during the combustion of organic material, from Lusakert Cave, a MP site in Armenia. We find no correlation between the abundance of light PAHs (3–4 rings), which are a major component of wildfire PAH emissions and are shown to disperse widely during fire events, and heavy PAHs (5–6 rings), which are a major component of particulate emissions of burned wood. Instead, we find heavy PAHs correlate with MP artifact density at the site. Given that hPAH abundance correlates with occupation intensity rather than lPAH abundance, we argue that MP hominins were able to control fire and utilize it regardless of the variability of fires in the environment. Together with other studies on MP fire use, these results suggest that the ability of hominins to manipulate fire independent of exploitation of wildfires was spatially variable in the MP and may have developed multiple times in the genus Homo.



The Beaver River Sandstone is a 10 s cm to 1.7 m thick silicified interval emplaced enigmatically within unconsolidated fluvial sand beds of the Lower Cretaceous McMurray Formation, the principle host rock of the Athabasca Oil Sands in northeastern Alberta. The silicified interval was partially eroded into during the Late Pleistocene as glacial meltwaters enlarged and deepened the Athabasca River Valley. The silcrete consists of a 10 s km long linear trend of discontinuous caprocks that sourced the innumerable quartzite boulders along the floor of the Athabasca River Valley. Siliceous cementation was concurrent with Aptian deposition of the McMurray Formation. The silicified bed extends along the disconformity between the lower and middle intervals of the McMurray Formation. The silicification at the end of lower McMurray deposition was spatiotemporally linked to regional dissolution of halite-anhydrite beds in Devonian Prairie Evaporite substrate, 200 m below. A sulphate-rich brine migrated up-section into the uppermost sand beds of the lower interval accumulated along topographic lows of the ancestral Athabasca River Valley, a segment of the regional Assiniboia Paleovalley. Near surface redox of the seep occurred by sulphate reducing microorganisms sourced from groundwater emanating from widespread peat mires. Strongly acidic groundwater resulted in corrosion of the quartz sand grains and silica saturated groundwater in the shallow subsurface. A pH shift occurred at onset of the middle interval, triggering silica cementation as the acidic seep mixed with meteoric-charged oxygenated groundwater along topographic lows of the river valley. Microbial filaments of unknown taxonomic affinity, now silicified, are the first recognized in the McMurray Formation oil sands. These microfossils consist of silicified hollow branching sheaths covered with nanoscale bulbous protuberances that preserve stepped transition textures of hydrated silica into quartz crystallites. They are evidence of partial microbial controls on the sulphate redox process resulting in this unusual type of silcrete.

Bullock, L., Parnell, J., Muirhead, D., Armstrong, J., Schito, A., Corrado, S., 2019. A thermal maturity map based on vitrinite reflectance of British coals. Journal of the Geological Society 176, 1136.


A compilation of new and previously published vitrinite reflectance (R0) data from Carboniferous coals constitutes the most comprehensive map of reflectance across Great Britain. Values of R0 range from 0.38 to 3.29%, recording an ambient thermal maturity in the early oil window (standard reference point for reflectance studies), modified by elevated heat flow in northern England and along the Variscan orogenic front. The map provides a context for other geological datasets.Supplementary material: A statistical summary of vitrinite reflectance data is available at https://doi.org/10.6084/m9.figshare.c.4529969

Burwicz, E., Haeckel, M., 2020. Basin-scale estimates on petroleum components generation in the Western Black Sea basin based on 3-D numerical modelling. Marine and Petroleum Geology 113, 104122.


A new numerical model reconstructing the depositional history (98–0 Ma) of the Western Black Sea sub-basin is presented. The model accounts for changing boundary conditions (i.e. water depth, bottom water temperature, heat flow evolution over time) and estimates the rates and total amounts of the in-situ biogenic methane generation and thermally-driven organic matter maturation in the source rocks. The overall thermogenic and biogenic gas generation predicted by the model is estimated at ~1560 Gt and ~3100 Gt, respectively.

Burzynski, G., Dececchi, T.A., Narbonne, G.M., Dalrymple, R.W., 2020. Cryogenian Aspidella from northwestern Canada. Precambrian Research 336, 105507.


The Ediacaran period saw the appearance of the first widespread ecosystems dominated by complex multicellular forms, with the earliest examples inhabiting deep waters below the photic zone. Contrary to expectation, the first appearance of large members of the Ediacara biota is sudden, and no definitive precursors have been described from earlier Neoproterozoic rocks; this sudden appearance has long been an enigma. Cryogenian fossils from deep-water deposits immediately pre-dating Marinoan glacial deposits within the Mackenzie Mountains, NW Canada, document the earliest stages of the growth of subphotic benthic communities. Among the previously described “Twitya discs” from this locality are at least two examples of the Ediacaran form-taxon Aspidella Billings, 1872. These fossils represent a nearly 80 Ma range extension of Aspidella and possible forerunners of the benthic communities of the Ediacara biota.

Cadena, S., Aguirre-Macedo, M.L., Cerqueda-García, D., Cervantes, F.J., Herrera-Silveira, J.A., García-Maldonado, J.Q., 2019. Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico. Estuarine, Coastal and Shelf Science 230, 106433.


Coastal lagoons are important aquatic systems with strong physicochemical gradients, where the participation of microorganisms in biogeochemical cycles has been well recognised; however, to date, the microbial diversity and distribution in these environments remains under-investigated. Here, three distinguished regions (oligohaline, marine and the mixing) of a transitional coastal lagoon were explored to characterise the structure and composition of benthic microbial communities through 16S rRNA gene Illumina-sequencing, for both Bacteria and Archaea domains. Principal coordinate analysis showed differences in the community structure according to the analysed zones. PERMANOVA analysis evidenced that, of the measured variables, sample zonation and salinity were the main environmental factors explaining the variance of the prokaryotic assemblages. Differentially abundant microbial taxa were detected for each region of the lagoon by LEfSe analysis. Representative members of anaerobic methanogens/methanotrophs (Methanosaetaceae, ANME 1-b and WSA2) were enriched in the oligohaline sediments, while the coastal marine zone had a community represented mainly by Sandaracinaceae, Aminicenantes and Thaumarchaeota (Group-C3). The sediments in the mixing zone had higher abundance of Flavobacteriaceae, Syntrophobacteraceae and uncultured

Thermoplasmatales, Bathyarchaeota and Lokiarchaeota. This study expands the available information of the composition and distribution of uncultured Bacteria and Archaea in transitional coastal lagoons, contributing to a systematic understanding of the functioning of these ecosystems.

Cañavate, J.-P., van Bergeijk, S., Giráldez, I., González-Ortegón, E., Vílas, C., 2019. Fatty acids to quantify phytoplankton functional groups and their spatiotemporal dynamics in a highly turbid estuary. Estuaries and Coasts 42, 1971-1990.

https://doi.org/10.1007/s12237-019-00629-8

Phytoplankton community composition expresses estuarine functionality and its assessment can be improved by implementing novel quantitative fatty acid–based procedures. Fatty acids have similar potential to pigments for quantifying phytoplankton functional groups but have been far less applied. A recently created dataset containing vast information on fatty acids of phytoplankton taxonomic groups was used as reference to quantify phytoplankton functional groups in the yet undescribed Guadalquivir River Estuary. Twelve phytoplankton groups were quantitatively distinguished by iterative matrix factor analysis of seston fatty acid signatures in this turbid estuary. Those phytoplankton groups including species unfeasible for visual identification (coccoid or microflagellated cells) could be quantified when using fatty acids. Conducting monthly matrix factor analyses over a period of 2 years and the full salinity range of the estuary indicated that diatoms dominated about half of the phytoplankton community spatiotemporally. The abundance of Cyanobacteria and Chlorophytes was inversely related to salinity and little affected by seasonality. Euglenophytes were also more abundant at lower salinity, increasing their presence in autumn–winter. Coccolithophores and Dinophytes contributed more to phytoplankton community at higher salinity and remained little affected by seasonality. Multivariate canonical analysis indicated that the structure of the estuarine phytoplankton community was most influenced by salinity; secondly influenced by water temperature, irradiance, and river flow; and unaffected by nutrients. Fatty acids are especially suited for phytoplankton community research in high turbid estuaries and generate outcomes in synergy with those derived from classical pigment assessments.

Čanković, M., Žučko, J., Radić, I.D., Janeković, I., Petrić, I., Ciglenečki, I., Collins, G., 2019. Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake. Systematic and Applied Microbiology 42, 126016.


Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996–2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.

Cao, S.C., Jang, J., Jung, J., Waite, W.F., Collett, T.S., Kumar, P., 2019. 2D micromodel study of clogging behavior of fine-grained particles associated with gas hydrate production in NGHP-02 gas hydrate reservoir sediments. Marine and Petroleum Geology 108, 714-730.


Fine-grained particles (fines) commonly coexist with coarse-grained sediments that host gas hydrate. These fines can be mobilized by liquid and gas flow during gas hydrate production. Once mobilized, fines can clog pore throats and reduce reservoir permeability. Even where particle sizes are smaller than pore-throat sizes, clogs can form due to clusters of fines. For certain types of fines, particularly swelling clays, cluster sizes depend on pore-fluid chemistry, which changes as pore-fluid freshens during gas hydrate dissociation. Fines can also be concentrated by a moving gas/liquid interface, increasing the chances of pore-throat clogging regardless of fines type. To test the relative significance of these clogging mechanisms, 2D micromodel experiments have been conducted with different pore-throat widths (20, 40, 60 and 100 μm), single-phase pore-fluids (deionized water and 2M-sodium-chloride solution), and moving gas/liquid interfaces on specimens from Sites NGHP-02-09 and NGHP-02-16 (NGHP-02: National Gas Hydrate Program Expedition 02) as well as a selection of pure fines (silica silt, mica, calcium carbonate, diatoms, kaolin, and bentonite). Clogging depended on the ratio of particle-to-pore throat size, and also on pore-fluid chemistry because the pore-fluid chemistry changes effectively increased or decreased the fine's cluster size relative to the pore-throat width. These interactions can be predicted based on the fine's electrical sensitivity (defined by Jang and Santamarina, 2016). The fine-grained sediment component (grain size < 75 μm) from the primary gas hydrate reservoir layers at Sites NGHP-02-09 and −16 show clogging via blocking or size exclusion (sieving) due to the large particles. Clogs also formed due to bridging or blocking by clusters of the smaller particles. Clogging generally occurred for pore-water sediment concentrations so low (0.2% by mass or less), that it was difficult to resolve the enhanced clogging in the presence of the gas/liquid meniscus.

Cappelli, E.L.G., Clarke, J.L., Smeaton, C., Davidson, K., Austin, W.E.N., 2019. Organic-carbon-rich sediments: benthic foraminifera as bio-indicators of depositional environments. Biogeosciences 16, 4183-4199.

https://www.biogeosciences.net/16/4183/2019/

Fjords have been described as hotspots for carbon burial, potentially playing a key role within the carbon cycle as climate regulators over multiple timescales. Nevertheless, little is known about the long-term fate of the carbon that may become stored in fjordic sediments. One of the main reasons for this knowledge gap is that carbon arriving on the seafloor is prone to post-depositional degradation, posing a great challenge when trying to discriminate between an actual change in the carbon deposition rate and post-depositional carbon loss. In this study, we evaluate the use of modern benthic foraminifera as bio-indicators of organic carbon content in six voes (fjords) on the west coast of Shetland. Benthic foraminifera are known to be sensitive to changes in organic carbon content in the sediments, and changes in their assemblage composition therefore reflect synchronous variations in the quantity and quality of carbon reaching the seafloor. We identified four environments based on the relationship between benthic foraminiferal assemblages and organic carbon content in the sediments: (1) land-locked regions influenced by riverine and/or freshwater inputs of organic matter, namely the head of fjords with a restricted geomorphology; (2) stressed environments with a heavily stratified water column and sediments rich in organic matter of low nutritional value; (3) depositional environments with moderate organic content and mild or episodic current activity; and (4) marginal to coastal settings with low organic content, such as fjords with an unrestricted geomorphology. We conclude that foraminifera potentially provide a tool to disentangle primary organic carbon signals from post-depositional degradation and loss of organic carbon because of their environmental sensitivity and high preservation potential in the sedimentary record.

Carlson, R.W., Garçon, M., O’Neil, J., Reimink, J., Rizo, H., 2019. The nature of Earth’s first crust. Chemical Geology 530, 119321.


Recycling of crust into the mantle has left only small remnants at Earth’s surface of crust produced within a billion years of Earth formation. Few, if any, of these ancient crustal rocks represent the first crust that existed on Earth. Understanding the nature of the source materials of these ancient rocks and the mechanism of their formation has been the target of decades of geological and geochemical study. This traditional approach has

been expanded recently through the ability to simultaneously obtain U-Pb age and initial Hf isotope data for zircons from many of these ancient, generally polymetamorphic, rocks. The addition of information from the short-lived radiometric systems 146Sm-142Nd and 182Hf-182W allows resolution of some of the ambiguities that have clouded the conclusions derived from the long-lived systems. The most apparent of these is clear documentation that Earth experienced major chemical differentiation events within the first tens to hundreds of millions of years of its formation, and that Earth’s most ancient crustal rocks were derived from these differentiated sources, not from primitive undifferentiated mantle. Eoarchean rocks from the North Atlantic Craton and the Anshan Complex of the North China Craton have sources in an incompatible-element-depleted mantle that dates to 4.4–4.5 Ga. Hadean/Eoarchean rocks from two localities in Canada show the importance of remelting of Hadean mafic crust to produce Eoarchean felsic crust. The mafic supracrustal rocks of the Nuvvuagittuq Greenstone Belt are a possible example of the Hadean mafic basement that is often called upon to serve as the source for the high-silica rocks that define continental crust. Many, but not all, ancient terranes show a shift in the nature of the sources for crustal rocks, and possibly the physical mechanism of crust production, between 3.0–3.6 Ga. This transition may reflect the initiation of modern plate tectonics. Eoarchean/Hadean rocks from some terranes, however, also display compositional characteristics expected for convergent margin volcanism suggesting that at least some convergent margin related magmatism began in the Hadean. The persistence of isotopic variability in 142Nd/144Nd into the mid-Archean, and the eventual reduction in that variability by the end of the Archean, provides new information on the efficiency by which mantle convection recombined the products of Hadean silicate-Earth differentiation. The rate of crust production and recycling in the Hadean/Archean, however, is not resolved by these data beyond the observation that extreme isotopic compositions, such as expected for Hadean evolved, continent-like, crust are not observed in the preserved Eoarchean rock record. The lack of correlation between 142Nd/144Nd and 182W/184W variation in Archean rocks suggests that these two systems track different processes; the Sm-Nd system mantle-crust differentiation while Hf-W is dominated by core formation. The major silicate differentiation controlling Sm/Nd fractionation occurred at ∼4.4 Ga, possibly as a result of the Moon-forming impact, after the extinction of 182Hf.

Carroll-Nellenback, J., Frank, A., Wright, J., Scharf, C., 2019. The Fermi Paradox and the aurora effect: Exo-civilization settlement, expansion, and steady states. The Astronomical Journal 158, 117.

http://dx.doi.org/10.3847/1538-3881/ab31a3

We model the settlement of the Galaxy by space-faring civilizations in order to address issues related to the Fermi Paradox. We are motivated to explore the problem in a way that avoids assumptions about the agency (i.e., questions of intent and motivation) of any exo-civilization seeking to settle other planetary systems. We begin by considering the speed of an advancing settlement front to determine if the Galaxy can become inhabited with space-faring civilizations on timescales shorter than its age. Our models for the front speed include the directed settlement of nearby settleable systems through the launching of probes with a finite velocity and range. We also include the effect of stellar motions on the long-term behavior of the settlement front which adds a diffusive component to its advance. As part of our model we also consider that only a fraction, f, of planets will have conditions amenable to settlement by the space-faring civilization. The results of these models demonstrate that the Milky Way can be readily filled-in with settled stellar systems under conservative assumptions about interstellar spacecraft velocities and launch rates. We then move on to consider the question of the Galactic steady state achieved in terms of the fraction X of settled planets. We do this by considering the effect of finite settlement civilization lifetimes on the steady states. We find a range of parameters for which 0 < X < 1, i.e., the Galaxy supports a population of interstellar space-faring civilizations even though some settleable systems are uninhabited. In addition we find that statistical fluctuations can produce local overabundances of settleable worlds. These generate long-lived clusters of settled systems immersed in large regions that remain unsettled. Both results point to ways in which Earth might remain unvisited in the midst of an inhabited galaxy. Finally we consider how our results can be combined with the finite horizon for evidence of previous settlements in Earth's geologic record. Using our steady-state model we constrain the probabilities for an Earth visit by a settling civilization before a given time horizon. These results break the link between Hart's famous "Fact A" (no interstellar visitors on Earth now) and the conclusion that humans must, therefore, be the only technological civilization in the Galaxy. Explicitly, our solutions admit situations where our current circumstances are consistent with an otherwise settled, steady-state galaxy.



A portable device that integrates sampling and extraction is proposed in this work. The unit is fabricated using commercial and standardized elements which guarantees the construction reproducibility. Also, it is simple to be mounted and on-site deployed making possible the multi-site sampling. The device uses a commercial nylon membrane as extraction phase for the isolation of the target compounds, but it can be adapted to other flat sorptive phases thus expanding the applicability. Once mounted, the unit is stirred into the sample by means of a portable drill enhancing in that way the diffusion of the target analyte towards the extraction phase. The hydrodynamic behavior and the design have been optimized and the device has been finally used for the extraction benzophenones from swimming pool samples. These endocrine disruptive compounds are determined by liquid chromatography tandem mass spectrometry (LC–MS/MS) at concentrations as low as 0.1 μg/L with precision, expressed as relative standard deviation, better than 9.9%. The accuracy, calculated as relative recovery, was in the range from 74 to 111 % thus being considered appropriate.

Casas, Y.A., Duran, J.A., Schoeggl, F.F., Yarranton, H.W., 2019. Settling of asphaltene aggregates in n-alkane diluted bitumen. Energy & Fuels 33, 10687-10703.


The settling rate of asphaltene aggregates is a key design parameter for partial deasphalting processes, and yet few data and models are available for these systems. The settling rates of asphaltene aggregates were measured in two Western Canadian bitumens diluted with n-heptane or n-pentane at 21 °C and atmospheric pressure. The density and viscosity of the mixtures, the size distributions of the aggregates, and the fractal dimensions of the aggregates were also measured. The asphaltene aggregates settled as a zone, that is, all aggregates settled at the same rate. The settling rates increased with increasing n-alkane content, reached a maximum at approximately 75 wt % n-alkane and then decreased at higher dilutions. The maximum settling rate corresponded to the maximum aggregate diameter and fractal dimension. The maximum settling rate in n-pentane diluted bitumen was 2 orders of magnitude greater than in the same bitumen diluted with n-heptane. The difference was attributed to the lower density and viscosity of the medium, larger aggregates, and higher fractal dimensions in n-pentane versus n-heptane. The settling rates were modeled with Stokes’ law modified to include the fractal dimension of the aggregates. Since zone settling was observed, the settling rate was determined from a single average diameter applied to all of the aggregates. The Sauter mean diameter was found to provide the most consistent results for the diluted bitumen systems in this study. No other form of hindering was required to match the data. The model matched the measured settling rates to within 20% of the maximum settling rate. The model is sensitive to the fractal dimension of the aggregates, and therefore precise determination of the fractal dimension is critical or it must be tuned to match the settling data.

Catchpole, R.J., Forterre, P., 2019. The evolution of reverse gyrase suggests a nonhyperthermophilic last universal common ancestor. Molecular Biology and Evolution 36, 2737-2747.

https://doi.org/10.1093/molbev/msz180

Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG data set to date. Comprising 376 sequences, our data set allows for phylogenetic reconstructions of RG with unprecedented size and detail. These RG phylogenies are strikingly different from those of universal proteins inferred to be present in the LUCA, even when using the same set of species. Unlike such proteins, RG does not form monophyletic archaeal and bacterial clades, suggesting RG emergence after the formation of these domains, and/or significant horizontal gene transfer. Additionally, the branch lengths separating archaeal

and bacterial groups are very short, inconsistent with the tempo of evolution from the time of the LUCA. Despite this, phylogenies limited to archaeal RG resolve most archaeal phyla, suggesting predominantly vertical evolution since the time of the last archaeal ancestor. In contrast, bacterial RG indicates emergence after the last bacterial ancestor followed by significant horizontal transfer. Taken together, these results suggest a nonhyperthermophilic LUCA and bacterial ancestor, with hyperthermophily emerging early in the evolution of the archaeal and bacterial domains.



A fungal species was isolated from 100% soybean methyl ester (B100 SME) and identified as Aureobasidium pullulans. The yeast was evaluated for its ability to grow in and to biodegrade B100 SME, B0 ultra-low-sulfur diesel (ULSD), and B20 ULSD (80% v/v ULSD + 20% B100 SME) in microcosms containing fuel over Bushnell-Haas mineral salts medium. The presence of SME affected the fungal cell morphology and metabolism. After 25 days, fungal biomass at the fuel/water interface in microcosms containing B100 SME and B20 ULSD were 0.98 ± 0.18 mg mL−1 and 0.16 ± 0.05 mg mL−1, respectively. In the B100 SME microcosms the esters concentrations fell by 10%. It was possible to observe that A. pullulans was biodeteriogenic in B100 and B20, but not in B0.

Chang, Q., Peng, Y.e., Shi, B., Hu, S., Shuai, Q., 2019. Rapid screening of new organic sulfates and alkaloids in single plant cells using nanospray high-resolution mass spectrometry. Analytical Methods 11, 5359-5365.

http://dx.doi.org/10.1039/C9AY01573F

In this work, a method for the rapid screening of bioactive compounds with characteristic groups in single plant cells has been developed using nanospray high-resolution mass spectrometry (HR-MS). A nanospray capillary was used for single cell sampling and ionization analysis. The screening method was built on the fact that some metabolites were species-specific, which contained common chemical moieties, and the common fragment ions can be produced from them in mass spectrometry. Therefore, new metabolites with common chemical moieties can be screened out by tracing the daughter ions in targeted-MS2 spectra. Using this method, nineteen bioactive compounds in plant cells were identified, fourteen of which were newly discovered compounds, such as organic sulfated compounds (R–HSO4) in Raphanus sativus root and solanine alkaloids (R–C27H42NO) in potato sprouts. Without pretreatment and chromatographic separation, the method realizes systematic screening of bioactive compounds in plant cells and retains the original information of samples to the greatest extent. More importantly, the established method shows great potential in the discovery of new bioactive compounds especially labile compounds in single-cell metabolomics.

Chen, H., Luo, J., Liu, S., Yuan, Z., Guo, J., 2019. Microbial methane conversion to short-chain fatty acids using various electron acceptors in membrane biofilm reactors. Environmental Science & Technology 53, 12914-12922.

https://doi.org/10.1021/acs.est.8b06767

Given our vast methane reserves and the forecasted shortage of crude oil in the not too distant future, the conversion of methane into value-added liquid chemicals or fuels would be beneficial. The generated chemicals or fuels could augment the petroleum-dominated chemical market, and also satisfy the increasing demand for transportation fuels. While methane bioconversion to liquid chemicals has just been reported recently, there is limited understanding of the process. This study aims to clarify the potential electron acceptors that could support the process. Here we operated four membrane biofilm reactors (MBfRs) fed with nitrate, nitrite, oxygen at a relatively low rate, and oxygen at a relatively high rate, respectively, to study if they can support methane

bioconversion to short-chain fatty acids (SCFAs) and the associated microbiological features. All tested electron acceptors facilitated methane bioconversion to SCFAs (ranging from 1.1 to 36.7 mg acetate L–1 d–1, or 3.4 to 114.6 mg acetate d–1 m–2 of biofilm). The carbon efficiency was estimated to be 7.9 ± 1.4% to 148.5 ± 1.3%, with an efficiency higher than 100%, suggesting the assimilation of other carbon, very likely CO2, into the products. A low oxygen supply rate of 46.4 ± 2.3 mg O2 d–1 m–2 was found to be the most favorable among all the electron conditions provided according to the SCFAs production rate and also the carbon utilization efficiency. Microbial characterization revealed that completely different communities evolved in the respective reactors, suggesting diverse microbial pathways exist for methane bioconversion into value-added chemicals.

Chen, K., Hu, D., Zhang, X., Zhu, H., Sun, L., Li, M., Shen, Y., 2020. Minor Δ33S anomalies coincide with biotic turnover events during the Great Ordovician Biodiversification Event (GOBE) in South China. Global and Planetary Change 184, 103069.


In this study, we report multiple S-isotopic data (δ34S and Δ33S) of sedimentary pyrite in Early to Late Ordovician sections from South China. The results reveal two distinct groups of negative Δ33S anomalies during the Dapingian and Sandbian to Early Katian stages, which coincide with two faunal turnover events. The negative Δ33S values reflect the mixing of sulfides with strongly negative δ34S and positive Δ33S, and sulfide with strongly positive δ34S and positive Δ33S. This mixing scenario may have resulted from the impinging of deep anoxic waters onto the continental shelves possibly facilitated by sea-level rise. The temporal co-occurrence of negative Δ33S anomalies with intervals of faunal turnover in brachiopod assemblages of South China suggests that the encroachment of anoxic waters may have driven the diversity crises. Our results provide evidence for a dynamic mechanism linking the recurrent upwelling of deep anoxic waters and faunal turnovers during the Early to Late Ordovician.

Chen, Y., Xia, L., Liang, R., Lu, Z., Li, L., Huo, B., Li, G., Hu, Y., 2019. Advanced materials for sample preparation in recent decade. TrAC Trends in Analytical Chemistry 120, 115652.


Sample preparation is an important and initial procedure of most chemical analysis methods. Due to sample diversity, selection of appropriate adsorbent for efficient preparation of different samples turned out to be significant for their analysis. Reaping the benefits from rapid development of material science, in the last decade, some novel adsorption materials have shown superiority in sample pretreatment. These advanced materials either have outstanding selectivity and/or excellent adsorption capacity for a single target or can selectively adsorb multiple targets from complex matrix. Here, we reviewed and summarized the progress of advanced materials for sample preparation in the last decade. Furthermore, we also discussed the limitations and future trends of these advanced adsorbents. Overall, sample preparation is promoted theoretically and practically by the development and application of advanced materials.

Chen, Z., Zhang, C., 2019. The characteristics and hydrocarbon-generation model of Paleogene–Neogene System saline lacustrine facies source rocks in the Western Qaidam Basin, China. Journal of Petroleum Exploration and Production Technology 9, 2441-2447.

https://doi.org/10.1007/s13202-019-0676-z

To further understand the characteristics and hydrocarbon-generation model of Paleogene–Neogene System salt-lake facies source rocks in the Western Qaidam Basin, selecting argillaceous source rock samples from the Lower Ganchaigou Formation, the Upper Ganchaigou Formation, and the Upper Youshashan Formation in the Western Qaidam Basin, relevant experimental studies have been carried out, including pyrolysis of rocks, analysis of soluble components, and simulation of hydrocarbon generation and expulsion. According to the analysis of the experimental results, the selected sample thermal evolution degree stays in the low-mature–immature stage and shows good hydrocarbon-generation ability. There was a positive correlation between

chloroform bitumen “A,” moderate salt content and carbonate content, and cumulative liquid hydrocarbon production. The hydrocarbon-generation peaks of the Paleogene–Neogene salt-lake facies source rocks in the Western Qaidam Basin are significantly advanced compared to the traditional model. The result clearly defines the hydrocarbon-generation model of Paleogene–Neogene salt-lake facies source rocks in the study area, which is important to direct the oil and gas exploration in the Western Qaidam Basin.

Chénard, C., Wijaya, W., Vaulot, D., Lopes dos Santos, A., Martin, P., Kaur, A., Lauro, F.M., 2019. Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters. Scientific Reports 9, 16390.

https://doi.org/10.1038/s41598-019-52648-x

Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.



Flow-through fractures dominate the movement of fluids in a variety of natural as well as engineered subsurface systems. Microbial activities in fractured rock impact subsurface energy recovery, storage, and waste disposal. It has been recognized that understanding how the contrasting permeability between fracture and matrix interacts with microbial metabolism under thermal and hydrological gradients is key to effective utilization of the subsurface, yet such studies are sparse. Microorganisms mediate the production of hydrogen sulfide (also known as souring) in oil-bearing geological formations. We conducted a comprehensive experimental study of a novel 2D fractured rock system to understand these complex interactions and demonstrated how biofilm development can impact fracture flow, which subsequently feedbacks to moderate sulfidogenesis. Elevated temperature relevant to reservoir conditions interacted with the injection of cold fluid and formed a thermal gradient away from fractures, creating thermal niches for microbial activities in the fractured rock. Results showed that while fracture flows were dominant in the beginning, with time, growth of the biofilm in the fractures reduced permeability, effectively moderating the initial fracture–matrix contrast, and limited microbial accessibility to nutrients and subsequent reactions rates.

Cho, E., Riches, E., Palmer, M., Giles, K., Ujma, J., Kim, S., 2019. Isolation of crude oil peaks differing by m/z ∼0.1 via tandem mass spectrometry using a cyclic ion mobility-mass spectrometer. Analytical Chemistry 91, 14268-14274.


Mass spectrometry is widely used in studying the structures of compounds present in crude oil. In this study, a novel mass spectrometer incorporating a cyclic ion mobility separator was used to obtain tandem mass spectra of crude oil compounds in a narrow mass-to-charge ratio (m/z) window. Isolation of specific peaks was performed by combining quadrupole and ion mobility separation. As a result, peaks differing by an m/z value of

0.1 could be isolated. Tandem mass spectrometry with collision-induced dissociation was successfully performed to study the chemical structures of the isolated ions. A series of ions ranging from m/z 374 to m/z 384, differing by two hydrogen atoms but with the same number of carbons, were isolated and tandem mass spectra were obtained. The higher m/z precursor ions produced smaller fragment ions; this is explained by the reduced aromaticity owing to an increased number of hydrogen atoms. The ions at m/z 388 and 374, differing by a CH2 group, produced very similar fragmentation patterns. Overall, the data obtained from this study clearly demonstrate that the novel cyclic ion mobility-mass spectrometer is a powerful instrument that can provide tandem mass spectra of individual compounds constituting complex mixtures such as crude oils.


https://doi.org/10.1029/2019GB006226

Abstract We use an ultrahigh-resolution 15-T Fourier transform ion cyclotron resonance mass spectrometer to elucidate the compositional changes in Arctic organic aerosols collected at Ny-Ålesund, Svalbard, in May 2015. The Fourier transform ion cyclotron resonance mass spectrometer analysis of airborne organic matter provided information on the molecular compositions of aerosol particles collected during the Arctic spring period. The air mass transport history, combined with satellite-derived geographical information and chlorophyll concentration data, revealed that the molecular compositions of organic aerosols drastically differed depending on the origin of the potential source region. The protein and lignin compound populations contributed more than 70% of the total intensity of assigned molecules when the air masses mainly passed over the ocean region. Interestingly, the intensity of microbe-derived organics (protein and carbohydrate compounds) was positively correlated with the air mass exposure to phytoplankton biomass proxied as chlorophyll. Furthermore, the intensities of lignin and unsaturated hydrocarbon compounds, typically derived from terrestrial vegetation, increased with an increase in the advection time of the air mass over the ocean domain. These results suggest that the accumulation of dissolved biogenic organics in the Arctic Ocean possibly derived from both phytoplankton and terrestrial vegetation could significantly influence the chemical properties of Arctic organic aerosols during a productive spring period. The interpretation of molecular changes in organic aerosols using an ultrahigh-resolution mass spectrometer could provide deep insight for understanding organic aerosols in the atmosphere over the Arctic and the relationship of organic aerosols with biogeochemical processes in terms of aerosol formation and environmental changes.



Rationale: Approximately 7 million liters of Corexit® dispersants were applied during the 2010 Deepwater Horizon oil spill to facilitate the dispersion of crude oil. At the time of application, the exact chemical composition of Corexit® was relatively unknown. Characterization of Corexit® 9500 was performed using high‐resolution mass spectrometry to further understand the complexity of the nonionic surfactant components of this mixture.

Methods: Corexit®9500 was analyzed by ultra‐high‐performance liquid chromatography (UHPLC) coupled to a high resolution Orbitrap Fusion Lumos mass spectrometer operated in positive electrospray ionization mode and a charged aerosol detector. Chromatographic conditions were optimized to efficiently separate isobaric and isomeric compounds. Polyethoxylated nonionic surfactants in Corexit® 9500 were identified using the following criteria: accurate mass (<3 ppm), retention time, and homologue series; in addition, interpretation of high‐resolution tandem mass spectra was used to annotate tentative component structures.

Results: More than 2000 polysorbate nonionic surfactants in 87 homologue series were detected. Polysorbate surfactants were characterized by the type of molecular basis group (sorbitan, isosorbide, or fatty acid), degree

of esterification (n = 0–4), ester chain length (C6–C24), and ester saturation, in addition to polydispersion by ethoxylation. Isomeric compounds were differentiated by LC/HRMS/MS analysis with product ion assignment. Results from the charged aerosol detector showed that the diesters (23.9 ± 0.78%) were the most abundant component in Corexit® 9500 followed by dioctyl sodium sulfosuccinate (DOSS) (19.2 ± 1.5%), triesters (17.3 ± 1.5%), and monoesters (15.7 ± 2.3%).

Conclusions: Our analytical approach facilitated the characterization of polysorbate surfactants within Corexit® 9500 and allowed a systematic study to differentiate isomeric and isobaric compounds, when standards were not available. The characterized composition of Corexit® 9500 will facilitate future studies to determine the chemical and biological transformation kinetics and byproducts of Corexit® 9500 under environmental conditions.

Chua, Y.W., Wu, H., Yu, Y., 2019. Interactions between low- and high-molecular-weight portions of lignin during fast pyrolysis at low temperatures. Energy & Fuels 33, 11173-11180.


This study investigates the interactions between low- and high-molecular-weight portions of lignin during fast pyrolysis at 100–300 °C. Lignin was extracted via tetrahydrofuran (THF) into the THF-soluble and -insoluble fractions, which represent the low-molecular-weight (LMW) and high-molecular-weight (HMW) portions of lignin, respectively. As pyrolysis temperature increases, the char yield of the LMW lignin decreases more significantly than that of the HMW lignin. During fast pyrolysis, the experimentally measured char yields from the whole lignin are consistently higher than those calculated from the respective char yields of the LMW and HMW portions via addition, increasing from ∼0.5 wt % at 100 °C to ∼10.7 wt % at 300 °C. Such char yield differences provide direct evidence on the existence of interactions between the LMW and HMW portions of lignin during fast pyrolysis of the whole lignin. The results suggest that the formation of the liquid intermediate phase from the LMW portion suppresses the release of volatiles from both the LMW and HMW portions, resulting in a higher char yield during fast pyrolysis of the whole lignin. Experimental results further show that such interactions also result in changes in lignin char structures (especially at temperatures of >150 °C) because of enhanced polymerization reactions of oxygenated functional groups and aromatic structures with fused rings of 2–5. As a result, more condensed char structures are formed, as evidenced by the decreased atomic O/C and H/C ratios for the chars produced from the whole lignin pyrolysis.

Cichon-Pupienis, A., Littke, R., Froidl, F., Lazauskienė, J., 2020. Depositional history, source rock quality and thermal maturity of Upper Ordovician - Lower Silurian organic-rich sedimentary rocks in the central part of the Baltic Basin (Lithuania). Marine and Petroleum Geology 112, 104083.


This study provides a comprehensive geochemical and mineralogical characterisation of the fine-grained, organic matter-rich sedimentary rocks of the Lower Palaeozoic in the central part of the Baltic Basin (Western Lithuania). The primary objective was to deduce environmental conditions for the Lower Palaeozoic succession which is very well preserved in the Baltic Basin, while the secondary goal was to obtain information on maturation and thermal history of the rocks. The sample set covers different stratigraphic units of the Ordovician- Lower Silurian succession and was analysed with a wide range of different methods including elemental analysis, organic petrography, Rock-Eval pyrolysis, molecular geochemical analysis of saturated and aromatic hydrocarbon fractions, inorganic geochemistry, mineralogy (XRF, XRD analysis) and magnetic susceptibility (MS) of rock samples. Their integration allowed a determination of the redox conditions, paleoproductivity and clastic input during sediment deposition. The fine-grained sediments are dominated by clay minerals and quartz and to a lesser extent carbonate, pyrite and feldspar. Microscopic analysis revealed abundant solid bitumen and zooclasts. Biomarker data indicate a marine origin for the precursor organic matter. Maturity parameters revealed the presence of a thermal maturity ‘anomaly’ in the southwestern part of Lithuania, where the late phase of oil generation and possibly beginning of condensate-wet gas generation with corresponding maximum paleotemperatures of 140–180 °C has been reached. Bottom-water conditions varied

from oxic to anoxic/euxinic during deposition driven by interaction of climate states, water mass circulation and stratification, water geochemistry and sea bottom bathymetry. Four shaly horizons (at the Upper Ordovician Fjäcka and Mossen Fms., Silurian Dobele Fm., and near Llandovery-Wenlock boundary levels) were recognized as being formed in oxygen-depleted benthic settings as indicated by high TOC and TS contents, sedimentation features, high metal enrichment or degree of piritization. The deposition of highly organic matter-rich Silurian Dobele Fm. might have coincided with oceanic anoxia and Late Aeronian bioevent, accompanied by an upwelling regime with increased paleoproductivity. The interpreted coarsening upward trend at the Early Silurian Adavere Regional Stage terminates with fall in relative sea-level at the Llandovery-Wenlock boundary. The geochemical proxies near Llandovery/Wenlock boundary may reflect the perturbations in oceanic water geochemistry which in turn may have eventually led to Ireviken mass extinction event.


https://www.frontiersin.org/article/10.3389/fenvs.2019.00172

Over the past two decades, headwater streams of the northern hemisphere have shown increased amounts of dissolved organic carbon (DOC), coinciding with decreased acid deposition. The exact nature of the mechanistic link between precipitation composition and stream water DOC is still widely debated in the literature. We hypothesize that soil aggregates are the main source of stream water DOC and that DOC release is greater in organic rich, riparian soils vs. hillslope soils. To test these hypotheses, we collected soils from two main landscape positions (hillslope and riparian zones) from the acid-impacted Sleepers River Research Watershed in northeastern Vermont. We performed aqueous soil extracts with solutions of different ionic strength (IS) and composition to simulate changes in soil solution. We monitored dynamic changes in soil particle size, aggregate architecture and composition, leachate DOC concentrations, dissolved organic matter (DOM) characteristics by fluorescence spectroscopy and trends in bioavailability. In low IS solutions, extractable DOC concentrations were significantly higher, particle size (by laser diffraction) was significantly smaller and organic material was separated from mineral particles in scanning electron microscope observations. Furthermore, higher DOC concentrations were found in Na+ compared to Ca2+ solutions of the same IS. These effects are attributed to aggregate dispersion due to expanding diffuse double layers in decreased IS solutions and to decreased bridging by divalent cations. Landscape position impacted quality but not quantity of released DOC. Overall, these results indicate that soil aggregates might be one important link between Critical Zone inputs (i.e., precipitation) and exports in streams.

Clapham, M.E., 2019. Conservation evidence from climate-related stressors in the deep-time marine fossil record. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190223.

https://doi.org/10.1098/rstb.2019.0223

Conservation of marine species requires the ability to predict the effects of climate-related stressors in an uncertain future. Experiments and observations in modern settings provide crucial information, but lack temporal scale and cannot anticipate emergent effects during ongoing global change. By contrast, the deep-time fossil record contains the long-term perspective at multiple global change events that can be used, at a broad scale, to test hypothesized effects of climate-related stressors. For example, geologically rapid carbon cycle disruption has often caused crises in reef ecosystems, and selective extinctions support the hypothesis that greater activity levels promote survival. Geographical patterns of extinction and extirpation were more variable than predicted from modern physiology, with tropical and temperate extinction peaks observed at different ancient events. Like any data source, the deep-time record has limitations but also provides opportunities that complement the limitations of modern and historical data. In particular, the deep-time record is the best source of information on actual outcomes of climate-related stressors in natural settings and over evolutionary timescales. Closer integration of modern and deep-time evidence can expand the types of hypotheses testable

with the fossil record, yielding better predictions of extinction risk as climate-related stressors continue to intensify in future oceans.


https://doi.org/10.1017/S1473550418000526

Haughton crater in the Canadian Arctic has been extensively used as a Mars (and lunar) analogue over the past 20 years. Here we report on small scale, dark, semi-seasonal slope streaks formed by melt water flowing down the crater walls that we observed during the Mars Society-sponsored M160 expedition to the F-MARS facility on the NW rim of the crater. The streaks are formed by biofilms colonizing snow melt flowing from semi-permanent snow patches in Haughton crater on Devon Island and elsewhere in the Canadian Arctic. These features superficially resemble the dark slope streaks and recurring slope lineae (RSL) observed on Mars and may serve as analogues for wet models for their formation and a contrast with dry formation models. Their significance to astrobiology and planetary science is three-fold: (1) as examples of dark recurring streaks known to be associated with water they provide a benchmark to compare with Martian slope streaks and RSL. (2) The melt streaks may have potential as astrobiological analogues for wet models of slope streaks and RSL. (3) They are natural laboratories to study planetary protection issues associated with robotic and astronaut exploration of potential water-related slope features on Mars.

Coch, C., Juhls, B., Lamoureux, S.F., Lafrenière, M.J., Fritz, M., Heim, B., Lantuit, H., 2019. Comparisons of dissolved organic matter and its optical characteristics in small low and high Arctic catchments. Biogeosciences 16, 4535-4553.


Climate change is affecting the rate of carbon cycling, particularly in the Arctic. Permafrost degradation through deeper thaw and physical disturbances results in the release of carbon dioxide and methane to the atmosphere and to an increase in lateral dissolved organic matter (DOM) fluxes. Whereas riverine DOM fluxes of the large Arctic rivers are well assessed, knowledge is limited with regard to small catchments that cover more than 40 % of the Arctic drainage basin. Here, we use absorption measurements to characterize changes in DOM quantity and quality in a low Arctic (Herschel Island, Yukon, Canada) and a high Arctic (Cape Bounty, Melville Island, Nunavut, Canada) setting with regard to geographical differences, impacts of permafrost degradation, and rainfall events. We find that DOM quantity and quality is controlled by differences in vegetation cover and soil organic carbon content (SOCC). The low Arctic site has higher SOCC and greater abundance of plant material resulting in higher chromophoric dissolved organic matter (cDOM) and dissolved organic carbon (DOC) than in the high Arctic. DOC concentration and cDOM in surface waters at both sites show strong linear relationships similar to the one for the great Arctic rivers. We used the optical characteristics of DOM such as cDOM absorption, specific ultraviolet absorbance (SUVA), ultraviolet (UV) spectral slopes (S275–295), and slope ratio (SR) for assessing quality changes downstream, at base flow and storm flow conditions, and in relation to permafrost disturbance. DOM in streams at both sites demonstrated optical signatures indicative of photodegradation downstream processes, even over short distances of 2000 m. Flow pathways and the connected hydrological residence time control DOM quality. Deeper flow pathways allow the export of permafrost-derived DOM (i.e. from deeper in the active layer), whereas shallow pathways with shorter residence times lead to the export of fresh surface- and near-surface-derived DOM. Compared to the large Arctic rivers, DOM quality exported from the small catchments studied here is much fresher and therefore prone to degradation. Assessing optical properties of DOM and linking them to catchment properties will be a useful tool for understanding changing DOM fluxes and quality at a pan-Arctic scale.

Colbran, L.L., Gamazon, E.R., Zhou, D., Evans, P., Cox, N.J., Capra, J.A., 2019. Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Nature Ecology & Evolution 3, 1598-1606.

https://doi.org/10.1038/s41559-019-0996-x

Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes’ regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.

Collett, T.S., Boswell, R., Waite, W.F., Kumar, P., Roy, S.K., Chopra, K., Singh, S.K., Yamada, Y., Tenma, N., Pohlman, J., Zyrianova, M., 2019. India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Gas hydrate systems along the eastern continental margin of India. Marine and Petroleum Geology 108, 39-142.


The primary objectives of the India National Gas Hydrate Program Expedition 02 (NGHP-02) were to obtain new data on the occurrence of gas hydrate systems and to advance the understanding of the controls on the formation of gas hydrate accumulations in the offshore of India. In accordance with the ultimate overall goal of the NGHP effort to assess the energy resource potential of marine gas hydrates in India, particular focus was placed on the exploration and evaluation of gas hydrate occurrences at high saturations in sand-rich systems. NGHP-02 operations were conducted from 3-March-2015 to 28-July-2015 off the eastern coast of India and included logging while drilling (LWD) operations at 25 locations, and coring and wireline logging operations at 10 locations, in the Krishna-Godavari and Mahanadi Basins.

The formation of highly concentrated gas hydrate accumulations, which are more suitable for energy extraction, requires the presence of relatively coarse-grained sediments with porosity needed to support the migration and accumulation of gas, and the nucleation of gas hydrate. The results of downhole logging, coring and formation pressure testing operations during NGHP-02 have confirmed the presence of extensive sand-rich depositional systems throughout the deepwater portions of the Krishna-Godavari and Mahanadi Basins. Two areas of the Krishna-Godavari Basin, referred to as Areas B and C, contain substantial gas hydrate accumulations in sand-rich systems and therefore represent ideal candidate sites for future gas hydrate production testing.

This summary and technical report includes a comprehensive synthesis of the geologic, geophysical, geochemical, and physical property data acquired during NGHP-02 as it relates to the controls on gas hydrate occurrence, particularly with regards to sand-hosted accumulations. In the Mahanadi Basin, despite the confirmation of extensive reservoir capacity, gas supply at the NGHP-02 sites was insufficient to charge the reservoirs with gas hydrates. In the Krishna-Godavari Basin, extensive reservoir systems were confirmed with sediment grain-sizes ranging from coarse-silts to gravels. These reservoirs range from fully- to partially-filled with gas hydrate. The gas is determined to be from only microbial sources, and in part migrated into the reservoirs from deeper systems. The controls on gas hydrate occurrence are complex and varied; and include substantial reservoir heterogeneity and sufficient permeability throughout the reservoirs and seals that allowed pervasive fluid flow into and through the hydrate-bearing systems. These discoveries are the most significant confirmation of the exploration approach that focuses on direct detection of hydrate reservoirs supported by comprehensive petroleum systems analyses.

Collett, T.S., Kumar, P., Boswell, R., Waite, W.F., 2019. Preface: Marine gas hydrate reservoir systems along the Eastern Continental Margin of India: Results of the National Gas Hydrate Program Expedition 02. Marine and Petroleum Geology 108, 1-2.


The 2015 India National Gas Hydrate Program Expedition 02 (NGHP-02) was conducted to obtain new information on the occurrence of gas hydrate systems and to advance the understanding of geologic controls on the formation of gas hydrate accumulations in the offshore of India. The ultimate goal of the NGHP effort is to assess the energy resource potential of marine gas hydrates in India. The Guest Editors for this special thematic issue of the Journal of Marine and Petroleum Geology (JMPG) have worked with more than 100 scientists and engineers to prepare the 45 individual reports included in this special issue to address the operational and technical contributions of the NGHP-02 Expedition.

This thematic issue on natural gas hydrates in the offshore of India is built on the foundation of five previous JMPG thematic issues that focused on the scientific results of other marine gas hydrate expeditions. These foundational contributions include: (1) “Scientific Results of the 2005 USDOE-Chevron JIP Drilling for Methane Hydrates Objectives in the Gulf of Mexico” (Volume 25, Issue 9, November 2008), (2) “Resource and Hazard Implications of Gas Hydrates in the Northern Gulf of Mexico: Results of the 2009 Joint Industry Project Leg II Drilling Expedition” (Volume 34, Issue 1, June 2012), (3) “Scientific Results of the Second Gas Hydrate Drilling Expedition in the Ulleung Basin (UBGH2), East Sea of Korea” (Volume 47, November 2013), (4) “Geologic Implications of Gas Hydrates in the Offshore of India: Results of the National Gas Hydrate Program Expedition 01” (Volume 58, Part A, December 2014), and (5) “Gas Hydrate Drilling in Eastern Nankai” (Volume 66, Part 2, September 2015).

The NGHP-02 Expedition was conducted from 03-March- 2015 to 28-July- 2015 off the eastern coast of India. The first two months of the expedition were dedicated to establishing 25 new research sites that featured the drilling of a downhole logging hole at each site. The next three months of the NGHP-02 Expedition were dedicated to sediment coring and other downhole measurement operations at 10 of the sites established during the expedition's first phase. The results of downhole logging, coring and formation pressure testing operations during NGHP-02 have confirmed the presence of large, highly concentrated gas hydrate accumulations in coarse-grained, sand-rich depositional systems throughout significant portions of the Krishna-Godavari Basin.

Post expedition research and reporting efforts included collaborative analysis of the unprecedented number of shipboard acquired data sets and core samples obtained during NGHP-02. The presentation of the scientific results of the NGHP-02 Expedition has culminated in the publication of the NGHP Expedition 02 Scientific Results Volume, which is represented by this Special Issue of the JMPG.

This Special Issue features a series of four reports that summarize the operational and scientific results of NGHP-02 Expedition that are presented in the 41 technical reports included this Special Issue. The first summary report, “India National Gas Hydrate Program Expedition 02: Operational and Technical Summary,” focuses on reviewing the tools and operational procedures for the NGHP-02 Expedition that led to the acquisition of an unprecedented amount of high-quality downhole logging and core data from numerous pore-filling, fracture-filling, and sediment-displacement types of gas hydrate occurrences. The summary report titled “India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Gas Hydrate Systems Along the Eastern Continental Margin of India” documents gas hydrate occurrences discovered during the NGHP-02 Expedition and examines geologic controls on the gas hydrate systems along the eastern continental margin of India. The “India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Evaluation of Natural Gas Hydrate-Bearing Pressure Cores” summary report presents a systematic review of select findings and implications of the coordinated pressure-core evaluation program as described in numerous technical reports within this Special Issue. The summary report titled “India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Numerical Simulation of Reservoir Response to Depressurization” addresses the key issues associated with understanding the potential production response of two gas hydrate accumulations discovered during the NGHP-02 Expedition to scientific depressurization experiments.

The 41 technical reports that make up the heart of this Special Issue deal with analyses of one of the most extensive data sets ever collected on the occurrence of natural gas hydrates. The data and information included

in this Special Issue will have far-reaching impact on both gas hydrate-related research and other important topical science issues that reach beyond the borders of India. The technical reports included in this Special Issue have been organized into topical sections that focus on (1) pre-expedition drill-site evaluation and planning efforts in support of NGHP-02, (2) lithostratigraphic and paleoenvironmental studies of discovered gas hydrate accumulations, (3) physical properties of conventional cores recovered during the expedition, (4) geochemical controls on the occurrence of gas hydrate, (5) microbiological systems associated with the occurrence of gas hydrate, (6) the analysis of hydrate-bearing sediments recovered in pressure cores, (7) downhole log and seismic characterization of the hydrate research sites established during NGHP-02, and (8) modeling of the expected physical, chemical, and mechanical responses of NGHP-02 discovered gas hydrate accumulations to production.

The Guest Editors of this Special Issue are thankful to the Ministry of Petroleum & Natural Gas within the Government of India, Directorate General of Hydrocarbons (DGH), Oil and Natural Gas Corporation Limited (ONGC), Oil India Ltd, GAIL (India) Ltd, Indian Oil Corporation Ltd and all other National Gas Hydrate Program (NGHP) partner organizations for providing the opportunity to contribute to the NGHP-02 Expedition and this special issue of the Journal of Marine and Petroleum Geology. The technical and science support from Japan Agency for Marine-Earth Science and Technology (JAMSTEC), the United States Geological Survey (USGS), the United States Department of Energy (US-DOE), the National Institute of Advanced Industrial Science and Technology (AIST), Geotek Coring and Schlumberger is gratefully acknowledged. The editors are thankful to the management of the NGHP, DGH and ONGC for permission to publish the findings of the NGHP-02 Expedition in this Special Issue.

We also want to thank Drs. Massimo Zecchin and Max Qinhong Hu, Editors-in-Chief of the Journal of Marine and Petroleum Geology, for accepting our proposal for this Special Issue. Special thanks is also extended to the Journal Managers, Dhilip Kumar Perumal and Krishnaveni Kunchala, for keeping this publication on track.

We also extend our greatest appreciation to the authors and coauthors who contributed their research efforts to this project. We also acknowledge our colleagues that provided our authors with more than 150 individual technical reviews.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Connolly, R., Jambrina-Enríquez, M., Herrera-Herrera, A.V., Vidal-Matutano, P., Fagoaga, A., Marquina-Blasco, R., Marin-Monfort, M.D., Ruiz-Sánchez, F.J., Laplana, C., Bailon, S., Pérez, L., Leierer, L., Hernández, C.M., Galván, B., Mallol, C., 2019. A multiproxy record of palaeoenvironmental conditions at the Middle Palaeolithic site of Abric del Pastor (Eastern Iberia). Quaternary Science Reviews 225, 106023.


This paper presents a multiproxy palaeoenvironmental study from Abric del Pastor (Alcoy, Spain), a rock shelter which has yielded evidence for Middle Palaeolithic human occupation. The sedimentary sequence has been analysed for lipid biomarker n-alkane abundances (ACL, CPI), compound specific leaf wax δ2H and δ13C, and bulk organic geochemistry (TOC, %N, %S), providing a record of past climate and local vegetation dynamics. Site formation processes have been reconstructed through the application of soil micromorphology. Analyses of anthracological, microvertebrate and macrofaunal assemblages from selected subunits are also presented here. Our data indicates that a variable climate marked by predominantly cold conditions persisted through most of the sequence and that Neanderthal occupations in stratigraphic unit IVd, assigned to MIS 4 or late MIS 5, occurred in a landscape setting characterised by a mosaic of biotopes. The presence of key resources inside the ravine where the site is located suggests that the occupation of the rock shelter may have been strategically motivated by a subsistence and mobility strategy which focused on zones of localised ecological resilience, such as intra-mountainous valleys or ravines, during periods of global or regional environmental downturn.

Cooper, B.T., Yan, X., Simón-Manso, Y., Tchekhovskoi, D.V., Mirokhin, Y.A., Stein, S.E., 2019. Hybrid search: A method for identifying metabolites absent from tandem mass spectrometry libraries. Analytical Chemistry 91, 13924-13932.


Metabolomics has a critical need for better tools for mass spectral identification. Common metabolites may be identified by searching libraries of tandem mass spectra, which offers important advantages over other approaches to identification. But tandem libraries are not nearly complete enough to represent the full molecular diversity present in complex biological samples. We present a novel hybrid search method that can help identify metabolites not in the library by similarity to compounds that are. We call it “hybrid” searching because it combines conventional, direct peak matching with the logical equivalent of neutral-loss matching. A successful hybrid search requires the library to contain “cognates” of the unknown: similar compounds with a structural difference confined to a single region of the molecule, that does not substantially alter its fragmentation behavior. We demonstrate that the hybrid search is highly likely to find similar compounds under such circumstances.

Cotrufo, M.F., Ranalli, M.G., Haddix, M.L., Six, J., Lugato, E., 2019. Soil carbon storage informed by particulate and mineral-associated organic matter. Nature Geoscience 12, 989-994.

https://doi.org/10.1038/s41561-019-0484-6

Effective land-based solutions to climate change mitigation require actions that maximize soil carbon storage without generating surplus nitrogen. Land management for carbon sequestration is most often informed by bulk soil carbon inventories, without considering the form in which carbon is stored, its capacity, persistency and nitrogen demand. Here, we present coupling of European-wide databases with soil organic matter physical fractionation to determine continental-scale forest and grassland topsoil carbon and nitrogen stocks and their distribution between mineral-associated and particulate organic matter pools. Grasslands and arbuscular mycorrhizal forests store more soil carbon in mineral-associated organic carbon, which is more persistent but has a higher nitrogen demand and saturates. Ectomycorrhizal forests store more carbon in particulate organic matter, which is more vulnerable to disturbance but has a lower nitrogen demand and can potentially accumulate indefinitely. The share of carbon between mineral-associated and particulate organic matter and the ratio between carbon and nitrogen affect soil carbon stocks and mediate the effects of other variables on soil carbon stocks. Understanding the physical distribution of organic matter in pools of mineral-associated versus particulate organic matter can inform land management for nitrogen-efficient carbon sequestration, which should be driven by the inherent soil carbon capacity and nitrogen availability in ecosystems.

Creighbaum, A.J., Ticak, T., Shinde, S., Wang, X., Ferguson, D.J., 2019. Examination of the glycine betaine-dependent methylotrophic methanogenesis pathway: Insights into anaerobic quaternary amine methylotrophy. Frontiers in Microbiology 10, 2572. doi: 10.3389/fmicb.2019.02572.


Recent studies indicate that environmentally abundant quaternary amines (QAs) are a primary source for methanogenesis, yet the catabolic enzymes are unknown. We hypothesized that the methanogenic archaeon Methanolobus vulcani B1d metabolizes glycine betaine (GB) through a corrinoid-dependent GB:coenzyme M (CoM) methyl transfer pathway. The draft genome sequence of M. vulcani B1d revealed a gene encoding a predicted non-pyrrolysine MttB homolog (MV8460) with high sequence similarity to the GB methyltransferase encoded by Desulfitobacterium hafniense Y51. MV8460 catalyzes GB-dependent methylation of free cob(I)alamin indicating it is an authentic MtgB enzyme. Proteomic analysis revealed that MV8460 and a corrinoid binding protein (MV8465) were highly abundant when M. vulcani B1d was grown on GB relative to growth on trimethylamine. The abundance of a corrinoid reductive activation enzyme (MV10335) and a methylcorrinoid:CoM methyltransferase (MV10360) were significantly higher in GB-grown B1d lysates compared to other homologs. The GB:CoM pathway was fully reconstituted in vitro using recombinant MV8460, MV8465, MV10335, and MV10360. Demonstration of the complete GB:CoM pathway expands the

knowledge of direct QA-dependent methylotrophy and establishes a model to identify additional ecologically relevant anaerobic quaternary amine pathways.

Cruz Luque, M., Aguilera, R., 2019. Eagle Ford and Pimienta shales in Mexico: A case study. SPE Reservoir Evaluation & Engineering 22, 1305-1322.

https://doi.org/10.2118/189797-PA

Our objective in this paper is to highlight the potential of the Eagle Ford (Cretaceous) and Pimienta (Upper Jurassic) shales in Burgos Basin (Mexico) through a comparison with the Eagle Ford Shale in Texas. The comparison is a case study focused on real data and their interpretation, north and south of the border, including geochemistry, geology, production, and reservoir-engineering data.

Our overall approach includes the description of Eagle Ford data in Texas, as well as Eagle Ford and Pimienta data in the Burgos Basin. The geologic comparison is carried out using cross sections of the various formations and geophysical data. Geochemical and petrophysical data are compared using specialized crossplots. Production data are compared through rate transient analysis and by investigating the different flow periods observed in wells in both sides of the border. Reservoir-engineering aspects are compared using material-balance methods developed specifically for analyzing multipurpose shale petroleum reservoirs.

Results indicate that there are many similarities but also some differences between the Eagle Ford Shale in Texas and shales in Mexico. The geologic and seismic cross sections show that there is continuity of the Eagle Ford on both sides of the border. However, structural geology in Mexico tends to be more complex than that in Texas. The geological and geochemical descriptions also show important similarities in the rock mineralogy, and the quantity, quality, and maturity of the organic matter. Well-log data show the same pattern of distribution on modified Pickett plots, developed originally for evaluation of the Eagle Ford Shale in Texas. Production data in the Burgos Basin shales are characterized by long periods (several months or even years) of transient linear flow, something that compares well with the Eagle Ford in Texas. Specialized material-balance calculations, which consider multiple porosities, have been used in the Eagle Ford Shale in Texas and are shown to have similar application in the Burgos Eagle Ford and Pimienta shales. On the basis of the Eagle Ford Shale performance in Texas, and the similarities with Burgos shales, the conclusion is reached that there is significant potential in the Mexican Eagle Ford and Pimienta shales.

We present a comparison of the interpretation of real geoscience and engineering shale data collected on both sides of the border. The comparison is meaningful and suggests that the potential of shale reservoirs south of the border will be quite significant. Mexico should benefit from the lessons learned from the Texas Eagle Ford Shale.

Cui, Q., Ma, X., Nakabayashi, K., Nakano, K., Miyawaki, J., Al-Mutairi, A., Marafi, A.M.J., Al-Otaibi, A.M., Yoon, S.-H., Mochida, I., 2019. Changes in composition and molecular structures of atmospheric residues during hydrotreating. Energy & Fuels 33, 10787-10794.


Better understanding of the changes in composition and molecular structures of atmospheric residue (AR) during hydrotreating is important for improving the hydrotreating performance of AR. Hydrotreating of an AR was carried out in a series of fixed bed reactors loaded with hydrodemetallization (HDM) and hydrodesulfurization (HDS) catalysts. The AR and its products were fractionated into saturates, aromatics, resins, and asphaltenes (SARA) and analyzed by using the gel permeation chromatography with an ultraviolet detector (GPC–UV) and with an inductively coupled plasma mass spectrometer (GPC), X-ray diffraction (XRD), 13C nuclear magnetic resonance (13C NMR), and electron spin resonance (ESR). Hydrotreating not only decreased the contents of S, N, V, Ni, resins, and asphaltenes, but also changed the composition, structure, and distribution of the remaining resins and asphaltenes as well as the remaining S, N, V, and Ni compounds in AR products. Almost all metals (V and Ni) existed in both resin (47%) and asphaltene (53%) fractions of AR, whereas in the final hydrotreated product, more than 84% of the remaining metals, which are considered as the

most refractory metal compounds, were in the asphaltenes, especially those with larger molecular size. The metal compounds in resins were easier to be removed. The low HDM reactivity of the remaining metal compounds can be attributed to their larger molecular size, which inhibited their approach to the active sites of the catalysts.

Dai, G., Zhu, E., Liu, Z., Wang, Y., Zhu, S., Wang, S., Ma, T., Jia, J., Wang, X., Hou, S., Fu, P., Peterse, F., Feng, X., 2019. Compositional characteristics of fluvial particulate organic matter exported from the world's largest alpine wetland. Journal of Geophysical Research: Biogeosciences 124, 2709-2727.

https://doi.org/10.1029/2019JG005231

Wetlands are hot spots for particulate organic matter (POM) supply into rivers, which link the land-ocean transfer in the global carbon cycle. However, the source, composition, and seasonal variability of POM carried by wetland-draining rivers are poorly constrained. Here we combine bulk and source-specific biomarker analyses to investigate the fluvial POM biogeochemistry of the Black and White Rivers draining from the Zoige wetland. We find that POM was dominated by terrestrial organic matter including high-molecular-weight (HMW) lipids, branched glycerol dialkyl glycerol tetraethers, and lignin phenols. However, fluvial POM was rich in HMW lipids and poor in lignin phenols compared to the catchment soils, possibly due to hydrodynamic sorting and dissolution processes. While lignin phenol concentrations were higher in the wet season, HMW lipid concentrations were lower. Additionally, lignin phenols increased with total suspended solids, while HMW lipids decrease. These contrasts imply an enhanced input of lignin-rich particles from soil surface layers in the wet season, diluting HMW lipids. Compared with that in other rivers around the world with a higher forest coverage in the catchment, POM in the Black and White Rivers draining grass-dominated wetlands had a much higher ratio of HMW fatty acids to lignin phenols. Our results represent a benchmark study highlighting compositional characteristics of fluvial POM exported from the Zoige wetland and the divergent behavior of molecular components during fluvial transfer. Such information is vital for assessing future changes in the Zoige wetland, given its high vulnerability to climatic and land use changes.


http://www.sciencedirect.com/science/article/pii/S2468256X19300598

Coal-derived gas determined by stable carbon isotopes were found in Well HYC 1 in the Yingjisu Sag, which brings a new dawn for gas exploration in this sag. Thermal maturity of the source rocks ranges 0.50%–0.65%. According to the traditional views that industrial oil/gas accumulations can only be formed if the thermal maturity of the source rocks is over 0.70%, so the recoverable resources of coal-derived gas were only 24.5 × 109 m3, and there was no drilling in the last 15 years. The TOC values of the Jurassic coal-measure mudstone, carbonaceous mudstone, and coal in the Yingjisu Sag are similar to those in the Kuqa Depression. Both of them belong to medium quality source rocks; hence the potential of gas generation and accumulation is good. In the Yingjisu Sag, the Jurassic residual thickness is 1000–2000 m. The distribution area with the maximum thickness of coal is basically overlapped with the distribution areas with the maximum thickness of carbonaceous mudstone and dark mudstone. The continuous distribution area is about 8000 km2, which should be the richest and the most favorable exploration area for the coal-derived gas resource, wherein gas fields will be discovered in the future.

Dai, S., Kim, J., Xu, Y., Waite, W.F., Jang, J., Yoneda, J., Collett, T.S., Kumar, P., 2019. Permeability anisotropy and relative permeability in sediments from the National Gas Hydrate Program Expedition 02, offshore India. Marine and Petroleum Geology 108, 705-713.


Gas and water permeability through hydrate-bearing sediments essentially governs the economic feasibility of gas production from gas hydrate deposits. Characterizing a reservoir's permeability can be difficult because

even collocated permeability measurements can vary by 4–5 orders of magnitude, due partly to differences between how various testing methods inherently measure permeability in different directions and at different scales. This study uses a customized flow anisotropy cell to investigate geomechanical and hydrological properties of hydrate-bearing sediments focusing on permeability anisotropy (i.e., horizontal, kh, to vertical, kv, permeability ratio) and relative permeability. Two cores recovered during India's National Gas Hydrate Program Expedition 02 (NGHP-02) are tested in this study. Near in situ effective vertical stress, ∼ 2 MPa, the permeability anisotropy is approximately kh/kv = 1.86 for the “seal core” (from a fine-grained non-reservoir overburden sedimentary section) and kh/kv = 4.24 for the gas hydrate reservoir core with tetrahydrofuran (THF) hydrate saturation Sh = 0.8. Permeability anisotropy increases exponentially with effective vertical stress, as described by kh/kv = α(σv/MPa)β, with α = 1.6, β = 0.22 for seal sediment and α = 3, β = 0.5 for THF hydrate-bearing sediment. Results imply the measured permeability from permeameter tests with vertical flow may underestimate the reservoir's flow performance, which is mainly horizontal (radial) toward a vertical well. Hydrate in sediment increases the gas-entry pressure and residual water saturation, but decreases the water retention curve's shape factor (m), resulting in a steeper curve. Distributions of available pore space sizes for flow in sediment with and without THF hydrate (Sh = 0.8) follow a log-normal distribution. Hydrate formation decreases the apparent mean pore size from ∼10 μm to ∼2 μm, without evidently changing the pore size distribution's standard deviation. Gas hydrate dissociation increases effective permeability and relative permeability to gas.

Dang, C., Nghiem, L., Fedutenko, E., Gorucu, S.E., Yang, C., Mirzabozorg, A., Nguyen, N., Chen, Z., 2020. AI based mechanistic modeling and probabilistic forecasting of hybrid low salinity chemical flooding. Fuel 261, 116445.


Over the past decades, it has been widely shown that Low Salinity Waterflooding (LSW) outperformed High Salinity Waterflooding (HSW) in terms of higher oil recovery, particularly in combining with other conventional Enhanced Oil Recovery (EOR) methods such as chemical flooding to benefit from their synergies. This paper presents a novel approach to mechanistically model Hybrid Low Salinity Chemical Flooding, with: (1) development of a hybrid EOR concept from past decades; (2) utilizing a Multilayer Neural Network (ML-NN) artificial intelligent technique in a robust Equation-of-State reservoir simulator fully coupled with geochemistry; (3) systematic validation with laboratory data; and (4) uncertainty assessment of the LSW process at the field scale. Various parameters such as polymer, surfactant, and salinity can affect on the relative permeability simultaneously during hybrid recovery processes. To overcome this problem, the ML-NN technique was applied for multidimensional interpolation of the relative permeability. Additionally, ML-NN was used within a Bayesian workflow to capture the uncertainties in both history matching and forecasting stages of LSW at field scale. The proposed model indicated good agreements with various coreflooding experiments including HSW, LSW, and Low Salinity Surfactant flooding (LSS), where it can efficiently capture the complex geochemistry, wettability alteration, microemulsion phase behavior, and the synergies occurring in these hybrid processes.

Darvish Sarvestani, A., Ayatollahi, S., Bahari Moghaddam, M., 2019. Smart water flooding performance in carbonate reservoirs: an experimental approach for tertiary oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2643-2657.

https://doi.org/10.1007/s13202-019-0650-9

Smart water flooding as a developing technique utilizes modified water chemistry in terms of salinity and composition to prepare the best-suited brine composition for a specific brine/oil/rock system to obtain higher oil recovery efficiency. Huge amount of unrecovered oil is expected to be remained in carbonate reservoirs; however, few research works on incremental oil recovery during smart water injection in carbonate cores at reservoir condition are reported. Several core flooding tests using one of the Iranian carbonate reservoir rock are conducted to check the effectiveness of smart water injection for more oil recovery efficiency. The results reaffirm the positive effect of sulfate ions to play a key role for better smart water performance. Moreover, it

was concluded that the calcium ion concentration is not as effective as magnesium ion for the tests performed at reservoir condition. Synthetic sea water (high-salinity) flooding was considered as the base scenario which results in almost 63% oil recovery efficiency for secondary recovery scenario. Formation of micro-emulsions was found to be the main reason of additional pressure drop during low-salinity water flooding. This clearly showed that the diluted smart water injecting increases the ultimate oil recovery up to 4–12% for already water-flooded carbonate reservoirs.

Deaf, A.S., Tahoun, S.S., Gentzis, T., Carvajal-Ortiz, H., Harding, I.C., Marshall, J.E.A., Ocubalidet, S., 2020. Organic geochemical, palynofacies, and petrographic analyses examining the hydrocarbon potential of the Kharita Formation (Albian) in the Matruh Basin, northwestern Egypt. Marine and Petroleum Geology 112, 104087.


A recent study of selected samples from the Cretaceous (Albian) Kharita Formation of Egypt revealed very good to excellent source rock (SR) potential for six intraformational, organic-rich intervals. This work investigates the SR potential of the entire Kharita Formation across the Matruh Basin, using samples from two wells: the Abu Tunis 1X well from the central part of the basin, and the Siqeifa 1X well drilled on the eastern margin of the basin. More strongly reducing conditions were developed in the centre of the basin, and resulted in the deposition of more organic-rich shales by comparison to the less reducing conditions that prevailed on the eastern basin margin, where the shales contain less organic matter. Deltaic intraformational shales and carbonates in the Kharita Formation of Abu Tunis 1X constitute a significant 120 m net of the potential SR. The lower Kharita Formation contains 34 m net shale SR of good to very good/excellent organic richness, yielding values of 1.14–11.59 wt % total organic carbon (TOC). The organic matter has low Hydrogen Index (HI) values (184–389 mg HC/g TOC) and amorphous organic matter (AOM) and relatively high non-opaque phytoclast frequencies indicating mainly gas/oil-prone organofacies (kerogen Types III/II). The upper Kharita is rather important, containing 86 m net shale/carbonate SR that has fair to good organic richness (0.8–1.8 wt % TOC), and lower HI (126–250 mg HC/g TOC), a dominance of non-opaque phytoclasts, and subordinate AOM frequencies, which together indicate gas/oil-prone organofacies (kerogen III/II). In the Siqeifa 1X well, Kharita deltaic intraformational shales and shaley dolostones comprise 80 m net SR, which has mainly fair to good to less very good organic richness (0.8–2.1 wt % TOC), whilst low HI (93–220 mg HC/g TOC), dominance of non-opaque phytoclasts and subordinate AOM indicate gas-prone organofacies (kerogen Type III). A relative upward increase in deposition of lignite and coaly carbonaceous material supports a gas-prone organofacies. Whilst thermal maturity indices only point to immature to early mature (pre- to early oil-window) SRs in both the Abu Tunis 1X and Siqeifa 1X wells, hydrocarbon exploration focussing on this potential source rock may be justified in areas to the southeast of the Matruh Basin, where modelling indicates this unit may have reached the late mature oil- to main gas-generation windows.

DeBlase, A.F., Bruening, C.R., Lewis, W.K., Bunker, C.E., 2019. In situ diagnostic of supercritical fuel surrogates: Probing heterogeneous catalysis by collision-induced dissociation in a molecular beam tandem mass spectrometer. Energy & Fuels 33, 10861-10867.


High-speed flight is limited by the amount of heat absorbed by the aviation fuel in a thermal management system. One approach to increase the thermal capacity of the fuel is via endothermic heterogeneous catalysis within the heat exchanger (HEX). To optimize such chemistry, better tools are needed to probe the chemical composition inside the HEX in situ. Toward this aim, we demonstrate the first on-line analysis of supercritical fuel surrogates (n-hexane and n-dodecane) over a zeolite catalyst (H-ZSM-5) using tandem mass spectrometry (MS). In our approach, a supersonic expansion is generated directly from the supercritical state (200–1000 °C and 400–1000 psi) of the neat fluid to capture a “snapshot” of the reactive intermediates and products inside the reactor by isolating these species in the gas phases. A molecular beam is generated, which is ionized by 10 eV electron-impact ionization (EI), and the mass spectrum is acquired using a triple quadrupole mass spectrometer. Based on precursor scans, we distinguish between EI fragments and cracking products from the furnace.

Product scans from the triple quadrupole reveal a structural similarity between the EI fragments and pyrolysis products. By directly identifying the light C2 and C3 radicals from pyrolysis, our results corroborate those in our previous study [DeBlase, Energy Fuels 2018, 32, 12289], which suggested that C2 and/or C3 intermediates are the key building blocks for aromatic synthesis by supercritical alkane pyrolysis. We anticipate that the new tandem MS capability will be widely used for catalyst development and to study the endothermic chemistry of fuels.

Deepak, M., Kumar, P., Singh, K., Yadav, U.S., 2019. Techno-economic forecasting of a hypothetical gas hydrate field in the offshore of India. Marine and Petroleum Geology 108, 741-746.


The National Gas Hydrate Program 01 Expedition (2006) and the National Gas Hydrate Program 02 Expedition (2015) have established the presence of large deposits of gas hydrates in deep-water areas offshore India. This paper presents the results of a techno-economic study carried out for the development of a hypothetical gas hydrate field in the Krishna-Godavari (KG) Basin located along the eastern margin of India. Standard industry approaches have been used to carry out capital cost and operational cost estimates. Based on initial reservoir simulation modelling results, three cases have been considered to encompass the possible range of reservoir production responses. In the first case, 18 MMSCMD of gas is envisaged to be produced from 120 wells for a production period of 10 years. In the second case, 12 MMSCMD of gas is envisaged to be produced from the 120 wells for 16 years. In the third case, 6 MMSCMD of gas is envisaged to be produced from the 120 wells for 30 years. The production rates assumed in Case 3 best represents what is believed to be the most reasonable production rates as modeled for a gas hydrate accumulation (NGHP-02 Area B; Site NGHP-02-16) drilled during NGHP-02. For Case 1, an initial determination is that field development is economically viable for prevailing gas price of USD 7.67/MMBTU with NPV of 1921 MMUSD and IRR of 27.87% with a cost of production of USD 4.74/MMBTU. For Case 2, the study indicates that field development is viable with NPV of USD 986 MMUSD and IRR of 20.27% and cost of production of USD 5.8/MMBTU. For Case 3, the cost of production is USD 9/MMBTU. No production data is available for the gas hydrate accumulations discovered during NGHP-02 in the offshore of India; therefore, these techno-economic results generated in this study can only be validated after matching the results from future pilot production testing under actual field conditions.



The biogenicity of most of the putative Archean organic-walled microfossils discussed in the literature remains debated. Here, we report morphological and geochemical characterizations of an assemblage of microfossils isolated from the 3.46 Gyr-old Strelley Pool Formation (Western Australia), thereby providing a new set of data on the oldest authentic microfossils on Earth. Isolated microstructures/microfossils were studied by combining scanning electron microscopy imaging and elemental analyses, Raman spectroscopy and nanoscale secondary ion mass spectrometry (NanoSIMS). We identified four morphological types, namely filaments, films, spheroids and lenses. A minority of spheroids, films and lenses exhibits a continuous wall cell surface and high N concentrations and substantial P contents (as suggested by 31P−/12C2

− ionic ratios), i.e. exceptionally high morphological and geochemical preservation levels. In addition to the detection of P within microfossil walls, P was also found within micrometric patches in lenses exhibiting a fusiform shape. These patches may be remains of polyphosphate granules possibly formed during sporulation, suggesting, in turn, that cellular organization appeared as soon as 3.46 Gyr ago.

Demongeot, J., Seligmann, H., 2019. The Uroboros theory of life’s origin: 22-nucleotide theoretical minimal RNA rings reflect evolution of genetic code and tRNA-rRNA translation machineries. Acta Biotheoretica 67, 273-297.

https://doi.org/10.1007/s10441-019-09356-w

Theoretical minimal RNA rings attempt to mimick life’s primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring’s 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs partly derived from tRNA accretions, we predict positive associations between relative secondary structure similarities with rRNAs over tRNAs and genetic code integration orders of RNA ring anticodon cognate amino acids. Analyses consider for each secondary structure all nucleotide triplets as potential anticodon. Anticodons for ancient, chemically inert cognate amino acids are most frequent in the 25 RNA rings. For RNA rings with primordial cognate amino acids according to tRNA-homology-derived anticodons, tRNA-homology and coding sequences coincide, these are separate for predicted cognate amino acids that presumably integrated late the genetic code. RNA ring secondary structure similarity with rRNA over tRNA secondary structures associates best with genetic code integration orders of anticodon cognate amino acids when assuming split anticodons (one and two nucleotides at the spliced RNA ring 5′ and 3′ extremities, respectively), and at predicted anticodon location in the spliced RNA ring’s midst. Results confirm RNA ring homologies with tRNAs and CDs, ancestral status of tRNA half genes split at anticodons, the tRNA-rRNA axis of RNA evolution, and that single theoretical minimal RNA rings potentially produce near-complete proto-tRNA sets. Hence genetic code pre-existence determines 25 short circular gene- and tRNA-like RNAs. Accounting for each potential splicing position, each RNA ring potentially translates most amino acids, realistically mimicks evolution of the tRNA-rRNA translation machinery. These RNA rings ‘of creation’ remind the uroboros’ (snake biting its tail) symbolism for creative regeneration.

Deng, Y., 2019. Control effect of the gulf on marine petroleum. Petroleum Research 4, 283-294.


About 80% of the discovered oil reserves in the world are generated from marine source rocks (about 20% from lacustrine source rocks), and the main control factors of reservoir formation are quite different for various oil-bearing basins. Whereas, as seen from global basins, the most important and most common accumulation control factor is the oil source, i.e. the “source control” is the most important factor. Through exploring the formation conditions of marine source rocks, the major marine basins in the world are well investigated. The result shows that the Persian Gulf Basin, Western Siberia Basin, Mexico Gulf Basin, North Sea Basin, Atlantic Ocean Basin, East Africa Coast Basin, Sichuan Basin, Tarim Basin and Paleo-Tethys Ocean and other basins were all gulfs during the formation period of the main source rocks, three sides of these gulfs are lands, and the major gulfs had only one water channel (a minority had two-three water channels) connected to the ocean. The gulf is the most favorable estuary for river. After passing through the weathered and denuded area, the river dissolves a large number of minerals, and bring some elements (such as P, Fe and K) to the gulf as the main nutrients for aquatic organisms (such as algae), however, nutrients brought by oceanic upwelling is unable to reach the gulf. Due to limited seawater replacement and exchange between gulf and ocean, the concentration of nutrients is high, and thus guaranteeing the long-term production of aquatic organisms (such as algae). Gentle winds and waves in the gulf were favorable for the preservation of organic matters, and thus high-quality source rocks were well developed. Relationship between modern marine and lake organisms and river, further confirm that the main nutrients for aquatic organisms growth are from rivers on the land.

Denny, A.C., Orland, I.J., Valley, J.W., 2020. Regionally correlated oxygen and carbon isotope zonation in diagenetic carbonates of the Bakken Formation. Chemical Geology 531, 119327.


Diagenetic minerals preserve records of burial processes that overprint records of seawater chemistry and impact reservoir porosity. The Mississippian-Devonian aged Bakken Formation in the Williston Basin is a reservoir rock of economic importance whose productivity is affected by diagenetic carbonates, particularly dolomite-ankerite-series carbonates. To investigate how diagenetic carbonate alteration manifests in the Bakken and how that might change across the basin, a combined δ18O and δ13C isotope dataset for diagenetic carbonates

was collected by in situ SIMS analysis of 10-μm spots from nine drill holes covering a ∼250 km transect of the middle Bakken member. Observed core-to-rim isotopic variability in these small Fe-zoned dolomites and calcites frequently exceeds 10‰ in both δ18O and δ13C, indicating significant changes in thermal and chemical conditions during cementation. Individual ankeritic growth bands can be correlated across the basin by systematic similarities in minor-element compositions and isotope ratios. In the central part of the basin, δ18O and δ13C trends at sub-mm-scale decline consistently towards the rims of ankerite-series carbonates, which is interpreted to reflect mineral growth coincident with rising temperatures and an increasing organic contribution to inorganic carbon during burial. The most abrupt shifts in δ18O and δ13C (changes as large as 12‰ for δ18O and 6.5‰ for δ13C within distances < 15 μm) are observed along the basin margin, and are believed to preserve signals of hydrocarbon expulsion and fluid infiltration along basin margins. Based on the data, we conclude that ankerite-series carbonates preserve records of prolonged thermal and chemical processes that operated basinwide. The isotopic trends presented here show diagenetic rock evolution from shallow dolomite formation to deep burial ankerites, as well as the isotopic responses of carbonates to changing fluids and availability of organic δ13C. These results provide important constraints on how carbonate isotope records may be altered during burial in organic-rich sedimentary rocks and emphasize the need for caution in using bulk powder samples for geochemical analysis in carbonate systems.

Dickson, J.H., Oeggl, K.D., Kofler, W., Hofbauer, W.K., Porley, R., Rothero, G.P., Schmidl, A., Heiss, A.G., 2019. Seventy-five mosses and liverworts found frozen with the late Neolithic Tyrolean Iceman: Origins, taphonomy and the Iceman’s last journey. PLOS ONE 14, e0223752.

https://doi.org/10.1371/journal.pone.0223752

The Iceman site is unique in the bryology of the Quaternary. Only 21 bryophytes (mosses and liverworts) grow now in the immediate vicinity of the 5,300 year old Iceman discovery site at 3,210m above sea level in the Ötztal Alps, Italy. By contrast 75 or more species including at least ten liverworts were recovered as subfossils frozen in, on and around the Iceman from before, at and after his time. About two thirds of the species grow in the nival zone (above 3,000m above sea level) now while about one third do not. A large part of this third can be explained by the Iceman having both deliberately and inadvertently carried bryophytes during his last, fatal journey. Multivariate analyses (PCA, RDA) provide a variety of explanations for the arrivals of the bryophytes in the rocky hollow where the mummy was discovered. This is well into the nival zone of perennial snow and ice with a very sparse, non-woody flora and very low vegetation cover. Apart from the crucial anthropochory (extra-local plants), both hydrochory (local species) and zoochory (by wild game such as ibex of both local and extra-local species) have been important. Anemochory of mainly local species was of lesser importance and of extra-local species probably of little or no importance. The mosses Neckera complanata and several other ecologically similar species as well as a species of Sphagnum (bogmoss) strongly support the claim that the Iceman, took northwards up Schnalstal, South Tyrol, as the route of the last journey. A different species of bogmoss, taken from his colon is another indication the Iceman’s presence at low altitude south of Schnalstal during his last hours when he was first high up, low down and finally at over 3,000m.

Dierkes, G., Lauschke, T., Becher, S., Schumacher, H., Földi, C., Ternes, T., 2019. Quantification of microplastics in environmental samples via pressurized liquid extraction and pyrolysis-gas chromatography. Analytical and Bioanalytical Chemistry 411, 6959-6968.

https://doi.org/10.1007/s00216-019-02066-9

The quantification of microplastics (MP) in environmental samples is currently a challenging task. To enable low quantification limits, an analytical method has been developed combining pressurized liquid extraction (PLE) and pyrolysis GC-MS. The automated extraction includes a pre-extraction step via methanol followed by a subsequent PLE using tetrahydrofuran. For the most frequently used synthetic polymers polyethylene (PE), polypropylene (PP), and polystyrene (PS), limits of quantification were achieved down to 0.007 mg/g. Recoveries above 80% were attained for solid matrices such as soil and sediments. The developed method was applied for MP quantification in environmental samples such as sediment, suspended matter, soil, and sewage sludge. In all these matrices, PE and PP were detected with concentrations ranging from 0.03 to 3.3 mg/g. In

sewage sludge samples, all three polymers were present with concentration levels ranging between 0.08 ± 0.02 mg/g (PP) and 3.3 ± 0.3 mg/g (PE). However, especially for solid samples, the analysis of triplicates revealed elevated statistical uncertainties due to the inhomogeneous distribution of MP particles. Thus, care has to be taken when milling and homogenizing the samples due to the formation of agglomerates.

Dixit, G., Ram, H., Kumar, P., 2019. Origin of gas in gas hydrates as interpreted from geochemistry data obtained during the National Gas Hydrate Program Expedition 02, Krishna Godavari Basin, offshore India. Marine and Petroleum Geology 108, 389-396.


This report presents the result of geochemical studies carried out on cores recovered from Krishna-Godavari Basin (K-G Basin) during the National Gas Hydrate Program Expedition 02 (NGHP-02). NGHP-02 targeted gas hydrate accumulations in sand facies in the K-G Basin off the east coast of the Indian Peninsula. Three areas (Area B, Area C and Area E) in the K-G Basin were investigated. During this expedition, 10 research sites in K-G basin were cored and samples for geochemistry analysis were collected. High TOC/TN ratios indicate an input from terrestrial organic matter. Analysis of gas samples from pressure cores also acquired during NGHP-02 were composed of mostly methane. Carbon Isotopic studies show that methane gas sampled from recovered gas hydrate samples were derived from biogenic (microbial) sources. This list of factors appears to indicate that the gas associated with the recovered hydrate-bearing core samples were derived from a microbial source. However, the biogeochemical processes responsible for generating the microbial gases found with the recovered gas hydrates may not have been limited to current limits off the gas hydrate stability zone. It is important to note here that microbial process likely extend to more than 1 km deep into the basin, so gas coming from below the GH stability zone can still be from a microbial source. In addition, the microbial gas within the stability zone was likely in part recycled from hydrate accumulations that has passed through the base of the gas hydrate stability zone as a product of sedimentation, with the dissociated microbial gas migration again vertically in the section, entering the gas hydrate stability zone and reforming gas hydrates. Although the organic carbon required for in situ methanogenesis and gas hydrate formation is abundant in the shallow sedimentary section of the KG-Basin, the faulted, fractured, and deformed stratigraphy observed in the KG- Basin coupled with high pore filling gas hydrate saturations at many sites, suggests that advective processes may be contributing to the supply of methane to the gas hydrates in the KG- Basin. The possible migration of gas from greater depths is also supported by seismic evidence of through-going migration-pathways that can connect the gas hydrate system with deeper petroleum systems. It is important to note here that the deep conventional gas accumulations in the basin also contain microbially sourced gas.

Dodd, M.S., Papineau, D., Pirajno, F., Wan, Y., Karhu, J.A., 2019. Minimal biomass deposition in banded iron formations inferred from organic matter and clay relationships. Nature Communications 10, 5022.

https://doi.org/10.1038/s41467-019-12975-z

The cycling of iron and organic matter (OM) is thought to have been a major biogeochemical cycle in the early ferruginous oceans which contributed to the deposition of banded iron formations (BIF). However, BIF are deficient in OM, which is postulated to be the result of near-complete oxidation of OM during iron reduction. We test this idea by documenting the prevalence of OM in clays within BIF and clays in shales associated with BIF. We find in shales >80% of OM occurs in clays, but <1% occurs in clays within BIF. Instead, in BIF OM occurs with 13C-depleted carbonate and apatite, implying OM oxidation occurred. Conversely, BIF which possess primary clays would be expected to preserve OM in clays, yet this is not seen. This implies OM deposition in silicate-bearing BIF would have been minimal, this consequently stifled iron-cycling and primary productivity through the retention of nutrients in the sediments.

Dong, J., Eiler, J., An, Z., Wu, N., Liu, W., Li, X., Kitchen, N., Lu, F., 2020. Clumped and stable isotopes of land snail shells on the Chinese Loess Plateau and their climatic implications. Chemical Geology 533, 119414.


We report stable (δ13Cshell, δ18Oshell) and clumped isotope (Δ47) compositions of modern and last glacial fossil snail shell carbonates from the Luochuan and Weinan sections on the central and southern Chinese Loess Plateau (CLP). Our study reveals that the average Δ47 temperature (T47) of modern snails is consistent with monitored temperatures during the snail growing season at the studied locations and is ~10 °C higher than that of fossil snails from glacial time. Moreover, the average δ13Cshell of modern snails is more depleted than that of fossils. We argue that the δ13Cshell cannot record changes in plant communities (i.e., the C3/C4 ratio) on the CLP and may mainly indicate arid conditions with depleted values reflecting reduced aridity. Additionally, the reconstructed snail body water δ18O (δ18Owater) of modern snails is more enriched than δ18O in modern growing season precipitation and δ18Owater of fossils. This contrast may be related to the high degree of evaporative enrichment of environmental water 18O in the body/ingested by modern snails under warm conditions. Therefore, we suggest that using δ18Oshell to directly reconstruct the oxygen isotopes of precipitation is difficult and that higher δ18Oshell and δ18Owater values probably indicate higher environmental temperature/stronger evaporative enrichment on glacial-interglacial timescales on the CLP.



Organic-matter pores are considered to be the dominant contributor to total porosity in many shale reservoirs, and consequently much attention has been paid to investigate the factors influencing their generation, especially thermal maturity. Recent studies have shown that in addition to maturation of organic matter, other diagenetic processes also play important roles in evolution of pore systems, including compaction, mineral dissolution, and quartz cementation. This study investigates the effect of thermal maturity on porosity development in the siliceous Woodford Shale by integrating multiple techniques including helium pycnometry, low pressure gas (N2) adsorption, mercury injection capillary pressure, and field emission scanning electron microscopy (SEM) analyses. We compare samples from two long cores from Woodford Shale at different levels of thermal maturity, one in the early oil window (average calculated Ro = 0.69%) and the other in the wet gas window (average calculated Ro = 1.34%).

Porosity, pore size, type, and volume vary systematically with the thermal maturity increasing from early oil window to wet gas window. Porosity measured by helium pycnometry averages 4.1% for early oil window samples, and increased by approximately 50% for the wet gas window samples (average porosity =6.3%). Both pore size and pore throat size distributions display decreasing trends from early oil window to wet gas window. Petrographic examination of SEM images shows that pores developed between clay platelets dominate in the early oil window samples, and secondary organic-matter pores are the dominant pore type in wet gas window samples. Porosity shows no obvious correlation to TOC content in both oil window and gas window samples, but correlates positive to silica content, suggesting that silica content largely controls variations in porosity. Both silica nanospheres and microcrystalline quartz were observed and appear to be significant in preserving pores from compaction by forming rigid frameworks that prevent pores from collapsing. Generation of secondary organic-matter pores and preservation of primary pores by silica nanospheres account for the net porosity increase from early oil window to wet gas window.

Donnarumma, L., Appolloni, L., Chianese, E., Bruno, R., Baldrighi, E., Guglielmo, R., Russo, G.F., Zeppilli, D., Sandulli, R., 2019. Environmental and benthic community patterns of the shallow hydrothermal area of secca Delle Fumose (Baia, Naples, Italy). Frontiers in Marine Science 6, 685. doi: 10.3389/fmars.2019.00685.

https://www.frontiersin.org/article/10.3389/fmars.2019.00685

The occurrence of hydrothermal vent ecosystems at Secca delle Fumose, Pozzuoli Bay (Gulf of Naples), represented an opportunity to study the benthic assemblages under the thermal stress of hydrothermal emissions in a very shallow environment (9–14 m water depth). In autumn 2016, the macrobenthic community was sampled by scuba divers at four sites located in the Baia Underwater Archeological Park. Two sites were characterized by vent emissions (one with white bacterial mat scattered on the bottom and one with a yellow

substrate around a geyser opening) and two at about 100 m away, used as control. Sediment and interstitial water environmental variables were measured to determine their influence on the structure of macrobenthic assemblages. A total of 1,954 macrofaunal individuals was found, characterized by great differences in abundance and species richness among sites. This pattern was correlated to the dominance of a particular set of variables that drastically change in a very small spatial scale, from one site to another. The control sites, characterized by the highest percentage of gravel in the sediments (19.67 ± 2.6%) and normal level of major ions such as Ca2+, K+, and Mg2+ in the interstitial waters, showed the highest values of sinecological indices. The “white” hydrothermal site exhibited the lowest species richness, abundance and species diversity, influenced by low pH values (∼7.6), high temperatures (∼37.53°C) and by the highest total organic carbon content (TOC 34.78%) in the sediment. The “yellow” hydrothermal site, with sediment TOC equal to 30.03% and interstitial sulfide ions measuring 130.58 ppm, showed higher values of sinecological indices than those recorded at the “white” site. Therefore, taxonomic analysis revealed a high turnover between control and vents sites. This highlights the preference for hydrothermal vents by a few resistant species, such as the gastropod Tritia cuvierii and the polychaete Capitella capitata, confirming the role of the latter species as opportunistic in extreme environments like Secca delle Fumose.

Döring, M., Leuenberger, M.C., 2019. Comparison of Holocene temperature reconstructions based on GISP2 multiple-gas-isotope measurements. Climate of the Past Discussions 2019, 1-45.

https://www.clim-past-discuss.net/cp-2019-132/

Nitrogen and argon stable-isotope data extracted from ancient air in ice cores provides the possibility to reconstruct Greenland past temperatures when inverting firn-densification and heat-diffusion models (firn-models) to fit the gas-isotope data (δ15N, δ40Ar, δ15Nexcess). This study uses the Döring and Leuenberger (2018) fitting-algorithm coupled on two state of the art firn-models to fit multiple Holocene gas-isotope data measured on the GISP2 ice core. We present for the first time the resulting temperature estimates when fitting δ15N, δ40Ar and δ15Nexcess as single targets with misfits generally in the low permeg level. Whereas the comparison between the reconstructions using δ15N and δ40Ar shows a high agreement, the use of δ15Nexcess for reconstructing temperature is problematic due to higher statistical and systematic data uncertainty influencing especially multi-decadal to multi-centennial signals and results in an unrealistic temperature estimate that differs significantly from the two other reconstructions. We find evidence for systematic too high δ40Ar data in the early- and late-Holocene potentially caused by post coring gas-loss or an insufficient correction of this mechanism. Next, we compare the performance of the Goujon et al. (2003) firn-model and the Schwander et al. (1997) firn-model for Holocene temperature reconstructions. Besides small differences of the reconstructed temperature anomalies – potentially caused by slightly different implementation of firn physics and parameters in the two models – the reconstructed temperature anomalies are highly comparable. We were able to quantify the contribution of the firn-model difference to the uncertainty budget of our reconstruction. Furthermore the fractions of uncertainty on the reconstructed temperatures arising from the non-perfect reproducibility of the fitting algorithm and from the remaining final misfits (low permeg level) were quantified. Together with the published measurement uncertainty of the gas-isotope data and the analysis of the impact of accumulation-rate uncertainty on the reconstruction we were able to calculate the mean uncertainty (2σ) for the nitrogen and the argon based temperature estimates with 2σT = 0.80…0.88 K for T(δ15N), and 2σT = 0.87…1.81 K for T(δ40Ar), respectively. Finally, we compare our reconstructed temperatures to two recent reconstructions based on the same gas-isotope data as used here, but following different reconstruction strategies: first the study of Buizert et al. (2018), which uses a combination of δ18Oice-calibration and δ15N-fitting, and second the study of Kobashi et al. (2017), where δ15Nexcess was fitted in order to conduct the temperature reconstruction. We find generally higher agreement between our T(δ15N) estimate and the Buizert et al. (2018) temperature – in terms of variability and correlation in three investigated periodic-time bands (multi-decadal, multi-centennial and multi-millennial) – as if our T(δ15N) reconstruction is compared to the Kobashi et al. (2017) temperature. However, all three reconstruction strategies lead to distinct temperature realizations.

Durán-Viseras, A., Sánchez-Porro, C., Ventosa, A., 2019. Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern. International Journal of Systematic and Evolutionary Microbiology 69, 3636-3643.

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003675

An extremely halophilic archaeon, strain F13-25T, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. The novel strain had pink-pigmented, non-motile, coccoid cells. Optimal growth was achieved at 25 % (w/v) NaCl, pH 7.5 and 37 °C. Strain F13-25T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) most closely related to Halorientalis persicus D108T (97.6–99.2 % sequence similarity) and Halorientalis regularis TNN28T (95.9–98.8 %). On the basis of the results of rpoB′ gene sequence analysis, strain F13-25Twas also closely related to Halorientalis persicus IBRC-M 10043T (89.9 %) and Halorientalis regularis TNN28T (92.3 %). Relatedness values, computed using the Genome-to-Genome Distance Calculator, between strain F13-25Tand Halorientalis persicus IBRC-M 10043T and Halorientalis regularis IBRC-M 10760T were 34.6 and 36.2 %, respectively. Average nucleotide identity values based on orthoANI, ANIb and ANIm of strain F13-25T and Halorientalis persicus IBRC-M 10043T and Halorientalisregularis IBRC-M 10760T were 88.0 and 88.8, 87.1 and 87.6 %, and 89.2 and 89.6 %, respectively. All values were far below the threshold accepted for prokaryotic species delineation. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and one glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content was 65.7 mol% (genome). The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain F13-25Trepresents a novel species of the genus Halorientalis , for which the name Halorientalis pallida sp. nov., with type strain F13-25T(=CECT 9384T=IBRC-M 11176T), is proposed.


https://doi.org/10.1073/pnas.1908512116

Significance: Microorganisms can cooperate by secreting public goods that benefit local neighbors; however, the conditions that favor cooperative growth in the environment, and the way in which this growth alters microbes’ contribution to ecosystem functions, remain unexplored. Here, we show that cooperation mediates the degradation of polysaccharide particles recalcitrant to hydrolysis in aquatic environments. Combining experiments and models, we define the physiological and environmental parameters that mediate the transition from cooperation to competition. Cooperation emerges through the self-organization of cells into ∼10- to 20-µm clusters that enable uptake of diffusible hydrolysis products. When cooperation is required, the degradation of recalcitrant biopolymers can only take place when degraders exceed a critical cell concentration, underscoring the importance of microbial interactions for ecosystem function.

Abstract: The recycling of particulate organic matter (POM) by microbes is a key part of the global carbon cycle. This process is mediated by the extracellular hydrolysis of polysaccharides, which can trigger social behaviors in bacteria resulting from the production of public goods. Despite the potential importance of public good-mediated interactions, their relevance in the environment remains unclear. In this study, we developed a computational and experimental model system to address this challenge and studied how the POM depolymerization rate and its uptake efficiency (2 main ecosystem function parameters) depended on social interactions and spatial self-organization on particle surfaces. We found an emergent trade-off between rate and efficiency resulting from the competition between oligosaccharide diffusion and cellular uptake, with low rate and high efficiency being achieved through cell-to-cell cooperation between degraders. Bacteria cooperated by aggregating in cell clusters of ∼10 to 20 µm, in which cells were able to share public goods. This phenomenon, which was independent of any explicit group-level regulation, led to the emergence of critical cell concentrations below which degradation did not occur, despite all resources being available in excess. In contrast, when particles were labile and turnover rates were high, aggregation promoted competition and decreased the efficiency of carbon use. Our study shows how social interactions and cell aggregation determine the rate and efficiency of particulate carbon turnover in environmentally relevant scenarios.

Eccles, K.M., Pauli, B.D., Chan, H.M., 2019. The use of geographic information systems for spatial ecological risk assessments: An example from the Athabasca oil sands area in Canada. Environmental Toxicology and Chemistry 38, 2797-2810.

https://doi.org/10.1002/etc.4577

There is an acknowledged need in ecotoxicology for methods that integrate spatial analyses in risk assessment. This has resulted in the emergence of landscape ecotoxicology, a subdiscipline of ecotoxicology. However, landscape ecotoxicology has yet to become common practice in risk assessment due to the underdevelopment of techniques and a lack of standardized methods. In the present study, we demonstrate how geographic information systems (GISs) can serve as a standardized platform to integrate data, assess spatial patterns of ecotoxicological data for multiple species, and assess relationships between chemical mixture exposures and effects on biota for landscape ecotoxicological risks assessment. We use data collected under the Joint Oil Sands Monitoring Program in the Athabasca Oil Sands Region in Alberta, Canada. This dataset is composed of concentrations of contaminants including metals and polycyclic aromatic compounds, and health endpoints measured in 1100 biological samples, including tree swallows, amphibians, gull and tern eggs, plants, and mammals. We present 3 examples using a GIS as a platform and geospatial analysis to: 1) integrate data and assess spatial patterns of contaminant exposure in the region, 2) assess spatial patterns of exposures to complex mixtures, and 3) examine patterns of exposures and responses across the landscape. We summarize the methods used in the present study into a workflow for ease of use. The GIS methods allow researchers to identify hot spots of contamination, use georeferenced monitoring data to derive quantitative exposure‐response relationships, and assess complex exposures with more realism.

Edegbai, A.J., Schwark, L., Oboh-Ikuenobe, F.E., 2020. Nature of dispersed organic matter and paleoxygenation of the Campano-Maastrichtian dark mudstone unit, Benin flank, western Anambra Basin: Implications for Maastrichtian Trans-Saharan seaway paleoceanographic conditions. Journal of African Earth Sciences 162, 103654.


The Campano-Maastrichtian age is an important time in the geological evolution of Nigeria as it marked the re-establishment of the Trans-Saharan seaway that was broken due to Santonian inversion tectonics. In this paper, we conducted a high-resolution investigation of the dark mudstone unit of the Campano-Maastrichtian Mamu Formation exposed in 4-outcrops in the western segment of the Anambra basin, Nigeria, using multidisciplinary tools involving geochemistry, palynofacies, and microfabric analyses. Our objectives were to determine the nature of organic matter preserved in the sediments and the paleo-oxygenation conditions of the Trans-Saharan seaway. Our findings reveal that the Trans-Saharan seaway was of low salinity, characterized by the dominance of terrestrial organic matter in the more proximal marsh and bay sub-environments (organic facies C and CD) and mixed terrestrial – marine organic matter (organic facies BC and C) in the more distal central basin. Bottom water paleo-oxygenation was predominantly oxic. However, palynofacies and microfabric evidences as well as inferences from Fe-TS-TOC relationship suggests pyrite formation occurred in at least two phases. The first phase of syngenetic to early diagenetic pyrite formation, which was due to bacterial sulphate reduction that occurred in the anoxic zone below the sediment water interface, whereas secondary (late diagenetic) pyrite growth which formed the bulk of pyrite preserved occurred at the base of the bottom water. Furthermore, we hypothesize that pyrite formation occurred faster, and was better preserved in the central basin than in the other sub-environments. This is attributed to the presence of more reactive organic matter (marine palynomorphs), higher salinity (more sulphate), mineralogy (higher clay content), and microfabric (thinner lamination with low degree of bioturbation).

Egres, A.G., Hatje, V., Gallucci, F., Machado, M.E., Barros, F., 2019. Effects of an experimental oil spill on the structure and function of benthic assemblages with different history of exposure to oil perturbation. Marine Environmental Research 152, 104822.


The present study compared the short-term effects of a diesel oil spill on the strucure and function of nematode and macrobenthic assemblages between tidal flats with different history of exposure to oil perturbation. A manipulative field experiment was conducted, where oil exposed treatments were contrasted with controls, during four successive times, two before and two after the oil spills. During the oil spill the death and the presence of diverse debilitated macrofaunal organisms were observed in the oil treatments. However, 24 h later no significant changes were identified, suggesting that the impacted plots were quickly recolonized. Nematode assemblages showed a decrease in overall density and an increase of r-strategist traits such as non-selective deposit feeders and colonizers at perturbed treatments from one of the historically non-perturbed tidal flats. We discuss the mechanisms responsible by distinctive patterns of response observed between the two benthic components.


https://doi.org/10.1007/s11631-019-00330-4

Humic acid (HA) can adsorb onto mineral surfaces, modifying the physicochemical properties of the mineral. Therefore, understanding the sorption behavior of HA onto mineral surfaces is of particular interest, since the fate and transport of many organic and inorganic contaminants are highly correlated to HA adsorbed onto clay surfaces. Due to the extreme heterogeneity of HA, the extracted IHSS Leonardite humic acid (LHA) used in this work was fractionated using an ultrafiltration technique (UF) into different molecular size fractions (Fr1, > 0.2 µm; Fr2, 0.2 µm–300,000 daltons; Fr3, 300,000–50,000 daltons; Fr4, 50,000–10,000 daltons; Fr5, 10,000–1000 daltons). Equilibrium and the kinetics of LHA and fraction adsorption onto kaolinite and montmorillonite were investigated. The results demonstrated that the maximum adsorption capacity of LHA, Fr1, Fr2, Fr3, Fr4, and Fr5 was 5.99, 13.69, 10.29, 7.02, 5.98, and 5.09 on kaolinite while it was 8.29, 22.62, 13.17, 8.91, 8.62, and 5.69 on montmorillonite, respectively. The adsorption equilibrium data showed that the adsorption behavior of LHA and its fractions could be described more practically by the Langmuir model than the Freundlich model. The rate of humic acid fraction adsorption onto clays increased with decreasing molecular size fraction and increasing carboxylic group content. Pseudo-first- and second-order models were used to assess the kinetic data and the rate constants. The results explained that LHA and its fractions adsorption on clay minerals conformed more to pseudo-second-order.

El Ghamry, M.N., El Amawy, M., Hagag, W., 2020. The role of Late Cretaceous wrench tectonics in hydrocarbon endowment in El-Gindi Basin, northern Western Desert, Egypt. Marine and Petroleum Geology 112, 104093.


Detailed subsurface mapping and structural analysis of El-Gindi basin indicate the hydrocarbon potentiality of the Cretaceous reservoirs. El-Gindi basin is a Late Cretaceous-Eocene basin located at El-Fayium district, northeastern Western Desert of Egypt. The overwhelming impact of the Late Cretaceous wrench tectonics was evident during the inversion of the Jurassic-Early Cretaceous rift-related basins along the North Western Desert of Egypt and subsequent deposition of a thick succession of Eocene sediments (~6000 ft Apollonia Formation) within El-Gindi Basin. These tectonic events were developing the oil maturity and trapping through the Late Cretaceous reservoir sequences, Upper Bahariya Formation (Cenomanian) and the Abu Roash “G” Member (Turonian). The Gindi Fault, however, is a NW-trending basement feature breaching El-Gindi basin and bounding several deeper half grabens in the western half of El-Fayium district. It has been reactivated during the Cretaceous, Eocene and probably Oligocene-Early Miocene times, where extended northwestward to the Qarun Field at the footslopes of the Kattaniya inverted basin forming several oil traps along its strike. The Late Cretaceous dextral wrenching developed a regional system of ENE-oriented structural ridges such as Kattaniya and Silah (bounded El-Gindi basin to the north and south, respectively), associated with a series of NE-to ENE- oriented right-lateral strike-slip faults enclosing some structural closures in between. The development of such ridges causing regional subsidence and subsequent deposition of the Apollonia Formation creating several structural hydrocarbon traps. In addition, the structural closures formed between the ends of right-lateral strike-slip faults at Silah High became potential sites for hydrocarbon accumulation. The thermal maturity model of

El-Gindi basin suggests a phase of hydrocarbon expulsion occurred during or immediately after deposition of the Apollonia Formation, where the Lower and Upper Cretaceous sediments passing the oil window. According to the analysis of well cores, E-logs and seismic data, shallow marine to deltaic environments have been assigned for the Cenomanian-Turonian reservoir sediments. Moreover, the deposition within channels, point-bars and estuarine environments for the hydrocarbon bearing sandstone reservoirs within El-Gindi Basin was identified.

Elewa, A.M.T., Abdelhady, A.A., 2020. Past, present, and future mass extinctions. Journal of African Earth Sciences 162, 103678.


Enigmatic catastrophic events, involving mass extinction of life forms, have been recorded several times in the Earth history. In many cases, the causes and mechanisms of these major and minor mass extinctions can be traced via the fossil record. A synthesis of the available information is herein made on the major catastrophic events through Earth history to understand the processes in the past and present with speculation into the future. The selective nature of major mass extinctions from the fossil record indicates the vanishing of specific taxa and the survival of others. The sudden extinction of organisms is almost accompanied by a gradual disappearance of other forms, thus excluding any single cause for the killing mechanism. Consequently, the multiple causes’ scenario is the plausible mechanism responsible for the vanishing of biota through the history of the fossil record. On the other hand, the recovery of biota after mass extinctions is also an intriguing phenomenon, in which some groups had rapid recovery whereas others took a long time for a revival. Based on multiple pieces of evidence from Africa, the end Permian extinction and the extinction of some Quaternary megafauna may be related to severe drought. In addition, the current mass extinction is progressively underway; arising from multiple causes and mainly related to anthropogenic activities, widespread diseases, as well as the possibility of extraterrestrial impacts. Reevaluation of the magnitude of the extinction event is urgently needed to judge if these extinctions represent natural episodic fluctuation of the biodiversity curve or unexpected catastrophe. Analyses of invertebrate occurrence data revealed that taxa originated during stressful crises intervals have a wider geographic range size and lower extinction rates. Moreover, species durations, geographic range, and diversity are influencing each other. In addition, the ecological traits of a species may control their extinction pattern and recovery speed-limit. Furthermore, the wide geographical distribution provides potentially to survive mass extinctions. Therefore, narrower geographic-range taxa are facing higher extinction risk.

Ellis, B.M., Fischer, C.N., Martin, L.B., Bachmann, B.O., McLean, J.A., 2019. Spatiochemically profiling microbial interactions with membrane scaffolded desorption electrospray ionization-ion mobility-imaging mass spectrometry and unsupervised segmentation. Analytical Chemistry 91, 13703-13711.


Imaging the inventory of microbial small molecule interactions provides important insights into microbial chemical ecology and human medicine. Herein we demonstrate a new method for enhanced detection and analysis of metabolites present in interspecies interactions of microorganisms on surfaces. We demonstrate that desorption electrospray ionization-imaging mass spectrometry (DESI-IMS) using microporous membrane scaffolds (MMS) enables enhanced spatiochemical analyses of interacting microbes among tested sample preparation techniques. Membrane scaffolded DESI-IMS has inherent advantages compared to matrix-assisted laser desorption ionization (MALDI) and other IMS methods through direct IMS analyses of microbial chemistry in situ. This rapid imaging method yields sensitive MS analyses with unique m/z measurements when compared to liquid chromatography–electrospray ionization-mass spectrometry (LC–ESI-MS) via unmediated sampling by MMS DESI-IMS. Unsupervised segmentation imaging analysis of acquired DESI-IMS data reveals distinct chemical regions corresponding to intermicrobial phenomenon such as predation and communication. We validate the method by linking Myxovirescin A and DKxanthene-560 to their known biological roles of predation and phase variation, respectively. In addition to providing the first topographic locations of known natural products, we prioritize 54 unknown features using segmentation within the region of

predation. Thus, DESI-IMS and unsupervised segmentation spatially annotates the known biology of myxobacteria and provides functional exploration of newly uncharacterized small molecules.

Engler, J.-O., von Wehrden, H., 2019. ‘Where is everybody?’ An empirical appraisal of occurrence, prevalence and sustainability of technological species in the Universe. International Journal of Astrobiology 18, 495-501.

https://doi.org/10.1017/S1473550418000496

We use recent results from astrobiology, particularly the A-form of the Drake equation and combine it with data on the evolution of life on Earth to obtain a new assessment of the prevalence of technological species in our Universe. A species is technological if it is, in theory, capable of interstellar communication. We find that between seven and 300 technological species have likely arisen in the Milky Way until today, the current state of which however unknown. Assuming that we are currently alone in our Galaxy, we estimate that we would need to wait for roughly 26 million years for a 50% chance of another technological species to arise. By relating our results to the much-debated Fermi–Hart paradox, we discuss if and to what extent our results may help quantify the chances of humanity to manage the transition to a long-term sustainable path of existence.

Erhard, A., Wallman, J.J., Postler, L., Meth, M., Stricker, R., Martinez, E.A., Schindler, P., Monz, T., Emerson, J., Blatt, R., 2019. Characterizing large-scale quantum computers via cycle benchmarking. Nature Communications 10, 5347.

https://doi.org/10.1038/s41467-019-13068-7

Quantum computers promise to solve certain problems more efficiently than their digital counterparts. A major challenge towards practically useful quantum computing is characterizing and reducing the various errors that accumulate during an algorithm running on large-scale processors. Current characterization techniques are unable to adequately account for the exponentially large set of potential errors, including cross-talk and other correlated noise sources. Here we develop cycle benchmarking, a rigorous and practically scalable protocol for characterizing local and global errors across multi-qubit quantum processors. We experimentally demonstrate its practicality by quantifying such errors in non-entangling and entangling operations on an ion-trap quantum computer with up to 10 qubits, and total process fidelities for multi-qubit entangling gates ranging from 99.6(1)% 99.6(1)% for 2 qubits to 86(2)% 86(2)% for 10 qubits. Furthermore, cycle benchmarking data validates that the error rate per single-qubit gate and per two-qubit coupling does not increase with increasing system size.

Estes, E.R., Berti, D., Coffey, N.R., Hochella, M.F., Wozniak, A.S., Luther, G.W., 2019. Abiotic synthesis of graphite in hydrothermal vents. Nature Communications 10, 5179.

https://doi.org/10.1038/s41467-019-13216-z

Deciphering the origin, age, and composition of deep marine organic carbon remains a challenge in understanding the dynamics of the marine carbon cycle. In particular, the composition of aged organic carbon and what allows its persistence in the deep ocean and in sediment is unresolved. Here, we observe that both high and low temperature hydrothermal vents at the 9° 50′ N; 104° 17.5 W East Pacific Rise (EPR) vent field are a source for (sub)micron-sized graphite particles. We demonstrate that commonly applied analytical techniques for quantification of organic carbon detect graphite. These analyses thereby classify graphite as either dissolved or particulate organic carbon, depending on the particle size and filtration method, and overlook its relevance as a carbon source to the deep ocean. Settling velocity calculations indicate the potential for these (sub)micron particles to become entrained in the buoyant plume and distributed far from the vent fields. Thus, our observations provide direct evidence for hydrothermal vents acting as a source of old carbon to the deep ocean.

Eswayah, A.S., Hondow, N., Scheinost, A.C., Merroun, M., Romero-González, M., Smith, T.J., Gardiner, P.H.E., 2019. Methyl selenol as a precursor in selenite reduction to Se/S species by methane-oxidizing bacteria. Applied and Environmental Microbiology 85, e01379-19.

http://aem.asm.org/content/85/22/e01379-19.abstract

Abstract:

A wide range of microorganisms have been shown to transform selenium-containing oxyanions to reduced forms of the element, particularly selenium-containing nanoparticles. Such reactions are promising for the detoxification of environmental contamination and the production of valuable selenium-containing products, such as nanoparticles for application in biotechnology. It has previously been shown that aerobic methane-oxidizing bacteria, including Methylococcus capsulatus (Bath), are able to perform the methane-driven conversion of selenite (SeO3

2−) to selenium-containing nanoparticles and methylated selenium species. Here, the biotransformation of selenite by Mc. capsulatus (Bath) has been studied in detail via a range of imaging, chromatographic, and spectroscopic techniques. The results indicate that the nanoparticles are produced extracellularly and have a composition distinct from that of nanoparticles previously observed from other organisms. The spectroscopic data from the methanotroph-derived nanoparticles are best accounted for by a bulk structure composed primarily of octameric rings in the form Se8 − xSx with an outer coat of cell-derived biomacromolecules. Among a range of volatile methylated selenium and selenium-sulfur species detected, methyl selenol (CH3SeH) was found only when selenite was the starting material, although selenium nanoparticles (both biogenic and chemically produced) could be transformed into other methylated selenium species. This result is consistent with methyl selenol being an intermediate in the methanotroph-mediated biotransformation of selenium to all the methylated and particulate products observed.

Importance: Aerobic methane-oxidizing bacteria are ubiquitous in the environment. Two well-characterized strains, Mc. capsulatus (Bath) and Methylosinus trichosporium OB3b, representing gamma- and alphaproteobacterial methanotrophs, respectively, can convert selenite, an environmental pollutant, to volatile selenium compounds and selenium-containing particulates. Both conversions can be harnessed for the bioremediation of selenium pollution using biological or fossil methane as the feedstock, and these organisms could be used to produce selenium-containing particles for food and biotechnological applications. Using an extensive suite of techniques, we identified precursors of selenium nanoparticle formation and also found that these nanoparticles are made up of eight-membered mixed selenium and sulfur rings.



Low salinity waterflooding (LSW) is an effective method for enhancing the oil recovery from many reservoirs, and its success has been traced to a host of low salinity effects. In this work, we perform molecular dynamics simulations to study the feasibility of recovering oil trapped by nanopores by lowering the reservoir salinity. The oil is initially trapped by a slit nanopore, with a portion of the oil protruding from the pore entrance. After the reservoir salinity is lowered, the thin brine films that separate the oil and pore walls become thicker to drive some of the trapped oil out of the pore. We quantify the free energy profile of this process and clarify the underlying molecular mechanisms. Interestingly, the brine film growth is dominated by the water transport from the brine reservoir into the pore rather than by the depletion of ions from the brine film. These results provide molecular evidence that low salinity brines benefit the recovery of the oil trapped by nanopores. They highlight that when ion depletion from thin brine films is suppressed, the osmosis of water can play a fundamental role in the expansion of the brine films; thus, the enhanced oil recovery. The slow osmosis of water through thin brine films and thus the slow displacement of oil from the pore may help explain the anomalously slow oil recovery reported in micro-modeling experiments of LSW.


https://doi.org/10.1155/2019/9752623

In order to explore the development methods suitable for heterogeneous low permeability reservoirs and study the distribution characteristics of residual oil, photoetched glass and artificial core models with three permeability ratios of 1, 6, and 9 were prepared in this research. Three displacement schemes including polymeric surfactant flooding, polymeric surfactant with binary flooding, and binary flooding were designed at the same expenses to obtain the displacement mechanism of various residual oil saturations. The results show that the best displacement efficiency can be achieved by polymeric surfactant flooding, followed by polymeric surfactant with binary flooding, and binary flooding for the models with the same permeability ratio. Binary flooding mainly activates cluster and oil drop residual oils, polymeric surfactant with binary flooding mainly activates cluster, oil film, and column residual oils, whereas polymeric surfactant flooding mainly activates cluster, oil drop, and column residual oils. In addition, with the increase of the model permeability ratio, the recovery ratio of water flooding decreases, whereas the enhanced oil recovery and the variations in residual oil saturation gradually increase after carrying out different displacement measures. The viscoelastic and shearing effects of the polymeric surfactant flooding system can better displace the residual oil, assisting in the further development of heterogeneous low permeability reservoirs.

Farley, K.R., Metcalf, W.W., 2019. The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea. FEMS Microbiology Letters 366.

https://doi.org/10.1093/femsle/fnz216

A repertoire of sophisticated genetic tools has significantly enhanced studies of Methanosarcina genera, yet the lack of multiple positive selectable markers has limited the types of genetic experiments that can be performed. In this study, we report the development of an additional positive selection system for Methanosarcina that utilizes the antibiotic nourseothricin and the Streptomyces rochei streptothricin acetyltransferase (sat) gene, which may be broadly applicable to other groups of methanogenic archaea. Nourseothricin was found to inhibit growth of four different methanogen species at concentrations ≤300 μg/ml in liquid or on solid media. Selection of nourseothricin resistant transformants was possible in two genetically tractable Methanosarcina species, M. acetivorans and M. barkeri, using the sat gene as a positive selectable marker. Additionally, the sat marker was useful for constructing a gene deletion mutant strain of M. acetivorans, emphasizing its utility as a second positive selectable marker for genetic analyses of Methanosarcina genera. Interestingly, two human gut-associated methanogens Methanobrevibacter smithii and Methanomassillicoccus luminyensis were more sensitive to nourseothricin than either Methanosarcina species, suggesting the nourseothricin-sat gene pair may provide a robust positive selection system for development of genetic tools in these and other methanogens.

Feng, R., Chen, S., Pang, Y., 2019. Simultaneous determination of permeability and diffusivity subject to dynamic sorption in gas shales. International Journal of Coal Geology 216, 103294.


Gas storage and transport mechanisms are essential for the shale gas development, while the three critical parameters are fracture permeability, adsorption capacity, and diffusivity. However, significant errors on the measured permeability may occur due to the gas sorption in the pores during the lab tests, which also affects the in-situ pore pressure. In this paper, a new approach is proposed to simultaneously determine the permeability, adsorption capacity, and diffusivity based on a modified pressure transient technique in the shale formation. Results showed that the shale permeability would be overestimated by >27.3% for Barnett shale and 55.5% for Eagle Ford shale when ignoring the sorption effect. The factors leading to errors in the measured permeability is numerically investigated and it was found that the sorption effect on the measured permeability can be reduced by using short core samples. In addition, the volume of the reference cell should be at least 6 times larger than the pore volume of the sample in order to control the permeability error within 5%. This study provides a methodology which can be readily applied in simultaneous determination of gas permeability, gas storage, and gas diffusivity, and sheds lights on better understanding of the gas storage and transport mechanisms in gas shale reservoirs.


https://doi.org/10.3390/microorganisms7110581

Surfactants are a broad category of tensio-active biomolecules with multifunctional properties applications in diverse industrial sectors and processes. Surfactants are produced synthetically and biologically. The biologically derived surfactants (biosurfactants) are produced from microorganisms, with Pseudomonas aeruginosa, Bacillus subtilis Candida albicans, and Acinetobacter calcoaceticus as dominant species. Rhamnolipids, sophorolipids, mannosylerithritol lipids, surfactin, and emulsan are well known in terms of their biotechnological applications. Biosurfactants can compete with synthetic surfactants in terms of performance, with established advantages over synthetic ones, including eco-friendliness, biodegradability, low toxicity, and stability over a wide variability of environmental factors. However, at present, synthetic surfactants are a preferred option in different industrial applications because of their availability in commercial quantities, unlike biosurfactants. The usage of synthetic surfactants introduces new species of recalcitrant pollutants into the environment and leads to undesired results when a wrong selection of surfactants is made. Substituting synthetic surfactants with biosurfactants resolves these drawbacks, thus interest has been intensified in biosurfactant applications in a wide range of industries hitherto considered as experimental fields. This review, therefore, intends to offer an overview of diverse applications in which biosurfactants have been found to be useful, with emphases on petroleum biotechnology, environmental remediation, and the agriculture sector. The application of biosurfactants in these settings would lead to industrial growth and environmental sustainability.

Fernandes, D., Wu, Y., Shirodkar, P.V., Pradhan, U.K., Zhang, J., Limbu, S.M., 2020. Sources and preservation dynamics of organic matter in surface sediments of Narmada River, India – Illustrated by amino acids. Journal of Marine Systems 201, 103239.


The preservation process of organic matter (OM) in estuarine environments determines the recycling and sinking of nutrients. This process requires the identification of sources, degradation states and the main processes affecting OM transformations. Unfortunately, our understandingof the sources, degradation and factors affecting OM distribution in tropical rivers experiencing strong seasonality and monsoonal influence is still limited. This study examined the sources, degradation and factors affecting OM distribution along the Narmada River and its estuary during different seasons. Surface waters and sediments were analyzed seasonally for selected physico-chemical parameters and bulk compositions of sediments, together with amino acids (AA, including the bacterial biomarker, D-AA). The sources of OM were soils containing detrital terrestrial plant material, with C4 and C3 plants dominating the estuarine and riverine stations, respectively. The other sources of OM were in-situ production, together with bacteria and their remnants. Strong seasonality and monsoonal conditions control the sources and distribution of OM in the river. Higher concentrations of total hydrolysable amino acids (THAA) were observed in riverine stations, suggesting the presence of relatively fresher OM. The lower OC:SA ratios recorded in the estuarine sediments indicated a limited OM preservation in the studied river. Positive degradation index (DI) values were obtained during the pre-monsoon season, suggesting seasonal changes in OM diagenesis. Physical (strong tidal currents, rainfall, reduced water flow due to seasonal variations and shallow water depth within the estuary) and geochemical (mineral surface adsorption processes) factors control the distribution and transport of OM. Taken together, the sources, preservation and diagenesis of terrestrial OM along the Narmada River was controlled differentially by the strong seasonal variability of the region. Thus, under variable temporal conditions, tropical estuaries and rivers form important realms for examining, determining, evaluating and assessing OM in order to better interpret nutrient budgets of the seas and oceans.

Fillinger, S., de la Garza, L., Peltzer, A., Kohlbacher, O., Nahnsen, S., 2019. Challenges of big data integration in the life sciences. Analytical and Bioanalytical Chemistry 411, 6791-6800.

https://doi.org/10.1007/s00216-019-02074-9

Big data has been reported to be revolutionizing many areas of life, including science. It summarizes data that is unprecedentedly large, rapidly generated, heterogeneous, and hard to accurately interpret. This availability has also brought new challenges: How to properly annotate data to make it searchable? What are the legal and ethical hurdles when sharing data? How to store data securely, preventing loss and corruption? The life sciences are not the only disciplines that must align themselves with big data requirements to keep up with the latest developments. The large hadron collider, for instance, generates research data at a pace beyond any current biomedical research center. There are three recent major coinciding events that explain the emergence of big data in the context of research: the technological revolution for data generation, the development of tools for data analysis, and a conceptual change towards open science and data. The true potential of big data lies in pattern discovery in large datasets, as well as the formulation of new models and hypotheses. Confirmation of the existence of the Higgs boson, for instance, is one of the most recent triumphs of big data analysis in physics. Digital representations of biological systems have become more comprehensive. This, in combination with advances in machine learning, creates exciting new research possibilities. In this paper, we review the state of big data in bioanalytical research and provide an overview of the guidelines for its proper usage.

Forgan, D.H., 2019. The habitable zone for Earth-like exomoons orbiting Kepler-1625b. International Journal of Astrobiology 18, 510-517.

https://doi.org/10.1017/S1473550418000514

The recent announcement of a Neptune-sized exomoon candidate orbiting the Jupiter-sized object Kepler-1625b has forced us to rethink our assumptions regarding both exomoons and their host exoplanets. In this paper, I describe calculations of the habitable zone for Earth-like exomoons in the orbit of Kepler-1625b under a variety of assumptions. I find that the candidate exomoon, Kepler-1625b-i, does not currently reside within the exomoon habitable zone, but may have done so when Kepler-1625 occupied the main sequence. If it were to possess its own moon (a ‘moon–moon’) that was Earth-like, this could potentially have been a habitable world. If other exomoons orbit Kepler-1625b, then there are a range of possible semi-major axes/eccentricities that would permit a habitable surface during the main sequence phase, while remaining dynamically stable under the perturbations of Kepler-1625b-i. This is however contingent on effective atmospheric CO2 regulation.

Forgan, D.H., 2019. Predator-prey behaviour in self-replicating interstellar probes. International Journal of Astrobiology 18, 552-561.

https://doi.org/10.1017/S1473550419000053

The concept of a rapid spread of self-replicating interstellar probes (SRPs) throughout the Milky Way adds considerable strength to Fermi's Paradox. A single civilization creating a single SRP is sufficient for a fleet of SRPs to grow and explore the entire Galaxy on timescales much shorter than the age of the Earth – so why do we see no signs of such probes? One solution to this Paradox suggests that self-replicating probes eventually undergo replication errors and evolve into predator-prey populations, reducing the total number of probes and removing them from our view.

I apply Lotka-Volterra models of predator-prey competition to interstellar probes navigating a network of stars in the Galactic Habitable Zone to investigate this scenario. I find that depending on the local growth mode of both populations and the flow of predators/prey between stars, there are many stable solutions with relatively large numbers of prey probes inhabiting the Milky Way. The solutions can exhibit the classic oscillatory pattern of Lotka-Volterra systems, but this depends sensitively on the input parameters. Typically, local and global equilibria are established with prey sometimes outnumbering the predators. Accordingly, we find this solution to Fermi's Paradox does not reduce the probe population sufficiently to be viable.


https://doi.org/10.1038/s41467-019-12984-y

At subduction zones, most diamonds form by carbon saturation in hydrous fluids released from lithospheric plates on equilibration with mantle rocks. Although organic molecules are predicted among dissolved species which are the source for carbon in diamonds, their occurrence is not demonstrated in nature, and the physical model for crustal diamond formation is debated. Here, using Raman microspectroscopy, I determine the structure of carbon-based phases inside fluid inclusions in diamond-bearing rocks from the Alps. The results provide direct evidence that diamond surfaces are coated by sp2-, and sp3-bonded amorphous carbon and functional groups of carboxylic acids (e.g., carboxyl, carboxylate, methyl, and methylene), indicating the geosynthesis of organic compounds in deep hydrous fluids. Moreover, this study suggests diamond nucleation via metastable molecular precursors. As a possible scenario, with carbon saturation by reduction of carboxylate groups, I consider tetrahedral H-terminated C groups as templates for the growth of sp3-structured carbon.


https://doi.org/10.1017/S1473550419000065

The in situ detection of organic molecules in space is key to understanding the variety and the distribution of the building blocks of life, and possibly the detection of extraterrestrial life itself. Gas chromatography mass spectrometry (GC-MS) has been the most sensitive analytical strategy for organic analyses in flight, and was used on missions from NASA's Viking, Phoenix, Curiosity missions to ESA's Rosetta space probe. While pyrolysis GC-MS revealed the first organics on Mars, this step alters or degrades certain fragile molecules that are excellent biosignatures including polypeptides, oligonucleotides and polysaccharides, rendering the intact precursors undetectable. We have identified a solution tailored to the detection of biopolymers and other biomarkers by the use of liquid-based capillary electrophoresis and electrochromatography. In this study, we show that a capillary electrochromatography approach using monolithic stationary phases with tailor-made surface chemistry can separate and identify various polycyclic aromatic hydrocarbons, nucleobases and aromatic acids that could be formed under astrophysically relevant conditions. In order to simulate flyby organic sample capture, we conducted hypervelocity impact experiments which consisted of accelerating peptide-soaked montmorillonite particles to a speed of 5.6 km s−1, and capturing them in an amorphous silica aerogel of 10 mg cm−3 bulk density. Bulk peptide extraction from aerogel followed by capillary zone electrophoresis led to the detection of only two stereoisomeric peptide peaks. The recovery rates of each step of the extraction procedure after the hypervelocity impact suggest that major peptide loss occurred during the impact. Our study provides initial exploration of feasibility of this approach for capturing intact peptides, and subsequently detecting candidate biomolecules during flight missions that would be missed by GC-MS alone. As the monolith-based electrochromatography technology could be customized to detect specific classes of compounds as well as miniaturized, these results demonstrate the potential of the instrumentation for future astrobiology-related spaceflight missions.

Fukushi, K., Sekine, Y., Sakuma, H., Morida, K., Wordsworth, R., 2019. Semiarid climate and hyposaline lake on early Mars inferred from reconstructed water chemistry at Gale. Nature Communications 10, 4896.

https://doi.org/10.1038/s41467-019-12871-6

Salinity, pH, and redox states are fundamental properties that characterize natural waters. These properties of surface waters on early Mars reflect palaeoenvironments, and thus provide clues on the palaeoclimate and habitability. Here we constrain these properties of pore water within lacustrine sediments of Gale Crater, Mars, using smectite interlayer compositions. Regardless of formation conditions of smectite, the pore water that last interacted with the sediments was of Na-Cl type with mild salinity (~0.1–0.5 mol/kg) and circumneutral pH. To interpret this, multiple scenarios for post-depositional alterations are considered. The estimated Na-Cl concentrations would reflect hyposaline, early lakes developed in 104–106-year-long semiarid climates. Assuming that post-depositional sulfate-rich fluids interacted with the sediments, the redox disequilibria in secondary minerals suggest infiltration of oxidizing fluids into reducing sediments. Assuming no interactions,

the redox disequilibria could have been generated by interactions of upwelling groundwater with oxidized sediments in early post-depositional stages.

Gadelha, L.G., Frena, M., Damasceno, F.C., Santos, E., SantÀnna, M.V.S., Vinhas, M.A., Barreto, T.S.A., Alexandre, M.R., 2019. Distribution patterns of aliphatic hydrocarbons in sediments from a tropical estuarine system. Marine Pollution Bulletin 149, 110607.


The São Francisco River has historical and economic relevance to the development of Northeast Brazil. However, the dams and reservoirs located along the basin and anthropogenic activities have been affecting its estuary. Herein, 26 surface sediment samples were analyzed to access the origin and distribution of aliphatic hydrocarbons. Concentrations of these hydrocarbons ranged from 0.95 μg g−1 to 2.87 μg g−1 in the summer and from 0.22 μg g−1 to 1.49 μg g−1 in the winter. Diagnostic ratios and indexes indicate higher plants, bacteria, and petroleum as hydrocarbon sources. A positive correlation was also observed between ∑n-alkanes and total organic matter (0.25) and fine fraction (0.47) as well as a significant difference (p < 0.05) between long-chain n-alkanes in the two sampling periods. Although the concentrations found in this study were lower than those in the other impacted coastal zones, our results have indicated the possible presence of petroleum contamination mainly associated with the discharge of oil derivatives from boat activities.

Gai, Z.-K., Zhu, M., Donoghue, P.C.J., 2019. The circulatory system of Galeaspida (Vertebrata; stem-Gnathostomata) revealed by synchrotron X-ray tomographic microscopy. Palaeoworld 28, 441-460.


Micro-CT provides a means of nondestructively investigating the internal structure of organisms with high spatial resolution and it has been applied to address a number of palaeontological problems that would be undesirable by destructive means. This approach has been applied successfully to characterize the cranial anatomy of Shuyu, a 428 million-year-old galeaspid (jawless stem-gnathostome) from the Silurian of Changxing, Zhejiang Province, China. Here, we use the synchrotron X-ray tomographic microscopy (SRXTM) to further describe the circulatory system of the head of Shuyu. Our results indicate that the circulatory system of galeaspids exhibits a mosaic of primitive vertebrate and derived gnathostome characters, including a number of derived gnathostome characters that are absent from osteostracans — the group conventionally interpreted as the sister lineage of jawed vertebrates. Our study provides a rich source of information that can be used to infer and reconstruct the early evolutionary history of the vertebrate cardiovascular system.

Gan, H., Wang, H., Shi, Y., Ma, Q., Liu, E., Yan, D., Pan, Z., 2020. Geochemical characteristics and genetic origin of crude oil in the Fushan sag, Beibuwan Basin, South China Sea. Marine and Petroleum Geology 112, 104114.


The Fushan sag is an important petroleum-bearing unit in the Beibuwan Basin, South China Sea. However, genetic relationship between oil and source rocks has not been well understood. In this work, 43 mudstone samples and 22 crude oil samples in the sag were collected for molecular geochemical and isotopic analyses to investigate this relationship. The geochemical data shows that the mudstones in Liushagang formation have poor to good oil generation potential with TOC ranging from 0.45 to 2.19 wt% and the kerogen is mainly type

. Two types of crude oils were identified in this study. The first type of Group A oils including the subgroup ⅡA1 and subgroup A2 has the characteristics of low maturity with low saturated hydrocarbon content and lighter δ13C values in the Huachang uplift. The source rocks for the Group A oils were deposited under suboxic to oxic and freshwater environment containing more terrestrial higher plant and less angiosperm. The subgroup A1 oils in Els1

1 reservoirs are separated from subgroup A2 in the Els12 reservoirs by relatively lower maturity. The

subgroup A1 and subgroup A2 oils are closely related to the Els1 to Els21 and Els1

2 to Els21 source rocks,

respectively. While the second type of oils including Group B and Group C oils has higher level of maturity with higher saturated hydrocarbon content and heavier δ13C values. The source rocks of Group B oils were

deposited in a freshwater environment with lower salinity, and more angiosperms and terrestrial higher plants input than those of Group C oils. Two subgroups are divided in the Group B oils, of which subgroup B1 oils have higher maturity and their source rocks were deposited in lower salinity with more terrestrial higher plant input than that of subgroup B2 oils. The subgroup B1 oils occurring in the Els3

1 reservoirs from the Huachang uplift are likely related to Els3

1 source rocks, while subgroup B2 oils in the Els22 reservoirs from the southern

slope area of the Bailian subsag is linked with mixed source of Els22 and Els3

1 mudstones. The Group C oils are distributed in Els2

2 and Els31 reservoirs in the Huachang uplift and their oil source are from Els3

2 mudstones. Two petroleum plays are likely divided by the mfs in Els2 based on the oil-source correlation in the sag. Group B and Group C oils belong to the lower play, and Group A oils only occur in the upper play. The distribution and accumulation of different groups of oils are mainly controlled by the special two-layered tectonostratigraphic framework and the transport ability of fault zone in the sag. This study clarifies the types of oils, as well as the oil-source correlation and the spatial distribution of different groups of oils. The results could benefit the further petroleum exploration and resource evaluation in the sag.



https://doi.org/10.1155/2019/5164010

In order to explore the process of acid- and CO2-induced degradation of wellbore cement and the development of pre-existing leakage channels in wellbore cement under sulfate-rich geological CO2 storage conditions, wellbore cement samples were immersed in SO4

2--bearing brine solution for 7 days, and the samples after reacting with the low and circumneutral pH solutions were scanned by a micro-CT scanner. HCl+Na2SO4 solution was used to simulate the low-pH condition in deep formation waters and the possible existence of high sulfate ion content in deep formation waters. The acidification and carbonation results were compared, and the results given different pH values and different curing conditions were compared as well. The results show that the degradation of cement was related to the pH value of the reaction solution. There was a significant dissolution in the exterior of the cement sample after exposure to the low-pH solution, but the dissolution surrounding a penetrating borehole at the center of the sample (mimicking a leakage pathway within the wellbore cement in geological CO2 storage environment) was limited. Comparison between acidification and carbonation results in this study shows formation of a thick carbonate layer due to cement carbonation, and this layer was not observed in the acidification result. As for different curing conditions of cement samples, no significant difference in cement alteration depth was observed for the acidification case. For the carbonation case, precipitations in the borehole occurred in the cement sample cured at ambient pressure, while the cement sample cured at high pressure did not produce any precipitation in the borehole. This study provides valuable information on how low pH-induced corrosion and HCO3

--induced cement carbonation contribute to structure evolution of wellbore cement in SO4

2--bearing brine under geological CO2 storage environment.

Gao, H., Zhang, B., Fan, L., Zhang, H., Chen, G., Tontiwachwuthikul, P., Liang, Z., 2019. Study on diffusivity of CO2 in oil-saturated porous media under high pressure and temperature. Energy & Fuels 33, 11364-11372.


To figure out the influence of different factors on the diffusion of carbon dioxide (CO2) in oil-saturated porous media, an experimental method using a multifunctional core displacement instrument instead of a PVT Cell was proposed to monitor the pressure decay in ten cores (porous media) under high temperature from 20 to 80 °C and pressure from 15 to 30 MPa. Then, the traditional diffusion model and the improved diffusion model in this work without and with consideration of the influence of tortuosity were applied to calculate the diffusivity of CO2, respectively. Also, it can be found that the novel diffusion model can predict the pressure decay and the diffusivity of CO2 in porous media well, indicating that the proposed model in this work can be used as an effective method to predict the diffusion coefficient of CO2 in porous media. Additionally, the influences of tortuosity, temperature, and initial pressure on the diffusivity of CO2 in oil-saturated porous media were analyzed. The results showed that the tortuosity of porous media brings to a dramatic decrease of the diffusion

coefficient, and the increasing temperature and higher initial pressure benefit the diffusion of CO2 in porous media.

Garain, S., Mitra, D., Das, P., 2019. Detection of hydrocarbon microseepage-induced anomalies by spectral enhancements of Landsat 7 ETM+ images in part of Assam–Arakan Fold Belt, India. Journal of Petroleum Exploration and Production Technology 9, 2573-2582.

https://doi.org/10.1007/s13202-019-00747-w

Subsurface hydrocarbon traps are not correctly sealed, and hydrocarbons move vertically from the reservoir as invisible traces in the form of microseepages. Long-term hydrocarbon microseepages cause surface or near-surface alterations such as bleaching of red beds, enrichment of ferrous iron minerals and higher concentrations of clay and carbonate minerals in soils/rocks. Multi- and hyperspectral remote sensing data have successfully been used to detect such alterations in many parts of the world. In India, such studies have not been carried out till now. In this study, Landsat 7 ETM+ images have been used to find out hydrocarbon microseepage-bearing areas in part of Assam–Arakan Fold Belt in the northeastern part of India. Based on the spectral characteristics of the hydrocarbon microseepage-induced altered minerals, two spectral enhancement techniques, viz. principal component analysis (PCA) and band ratio analysis, have been carried out on the Landsat 7 ETM+ images. PCA reveals that three principal component images—1457PC3, 1345PC2 and 3457PC4—show relatively better enhancement for the hydrocarbon-bearing alteration areas. Again, band ratio analysis of the images indicates that ratio images—3/1, (2 + 5)/(3 + 4) and 7/5—show excellent spectral enhancement for the hydrocarbon-induced mineral alterations. The three PC images have been combined with the three band ratio images to find out probable hydrocarbon microseepage areas. The remote sensing-derived prospect areas have been validated with surface geochemical, seismic/geologic and gravity data available in the area.


https://doi.org/10.1007/s10933-019-00097-x

Peat bogs located in high mountains are suitable places to study local environmental responses to climate variability. These ecosystems host a large number of eukaryotes with diverse taxonomic and functional diversity. We carried out a metabarcoding study using universal 18S and COI markers to explore the composition of past and present eukaryotic communities of a Pyrenean peat bog ecosystem. We assessed the molecular biodiversity of four different moss micro-habitats along a flood gradient in the lentic Bassa Nera system (Central Pyrenees). Five samples collected from different sediment depths at the same study site were also analysed, to test the suitability of these universal markers for studying paleoecological communities recovered from ancient DNA and to compare the detected DNA sequences to those obtained from the modern community. We also compared the information provided by the sedimentary DNA to the reconstruction from environmental proxies such as pollen and macro-remains from the same record. We successfully amplified ancient DNA with both universal markers from all sediment samples, including the deepest one (~ 10,000 years old). Most of the metabarcoding reads obtained from sediment samples, however, were assigned to living edaphic organisms and only a small fraction of those reads was considered to be derived from paleoecological communities. Inferences from ancient sedimentary DNA were complementary to the reconstruction based on pollen and macro-remains, and the combined records reveal more detailed information. This molecular study yielded promising findings regarding the diversity of modern eukaryotic peat bog communities. Nevertheless, even though information about past communities could be retrieved from sediment samples, preferential amplification of DNA from living communities is a caveat for the use of universal metabarcoding markers in paleoecology.

García-Cicourel, A.R., van de Velde, B., Verduin, J., Janssen, H.-G., 2019. Comprehensive off-line silver phase liquid chromatography × gas chromatography with flame ionization and vacuum ultraviolet detection for the detailed characterization of mineral oil aromatic hydrocarbons. Journal of Chromatography A 1607, 460391.


Highly purified mineral oils used for the elaboration of pharmaceutical, food and cosmetic products can contain residual mineral oil aromatic hydrocarbons (MOAH). Quantification of the MOAH level as well as detailed characterization of the aromatic species present is important for safety evaluations and for optimization of the purification process. Two comprehensive off-line silver phase liquid chromatography × gas chromatography (AgLC × GC) methods, one with flame ionization detection (FID) and another with vacuum ultraviolet detection (VUV), were developed for MOAH analysis. The methods showed a better resolution between the MOSH and MOAH groups compared to the traditional online LC-GC methods due to the different retention mechanisms employed in the two dimensions, albeit that the gain was less than seen e.g. in edible oil analysis. An important advantage of the new comprehensive AgLC × GC methods is that the use of markers to determine the MOSH/MOAH cut-point is no longer needed, because all the eluent coming from the LC separation is transferred as narrow fractions to the GC. Due to the use of silver based stationary phases in the first separation dimension, a group-type separation of the mineral oil according to the degree of aromaticity (aliphatics, mono-aromatics and poly-aromatics) was obtained. Moreover, thanks to the use of VUV detection, the new method also delivered additional structural information on the different groups of compounds present.

Gibu, N., Kasai, D., Ikawa, T., Akiyama, E., Fukuda, M., 2019. Characterization and transcriptional regulation of n-alkane hydroxylase gene cluster of Rhodococcus jostii RHA1. Microorganisms 7, 10.3390/microorganisms7110479.


Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway—a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation—was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.

Gifford, D.R., 2019. Life on the frontline reveals constraints. Nature Ecology & Evolution 3, 1501-1502.

https://doi.org/10.1038/s41559-019-1010-3

The existence of trade-offs between traits under selection is a fundamental concept in evolutionary biology. Analysis of a densely sampled collection of adaptive mutations in yeast reveals that no single mutation can allow it to overcome detected trade-offs between key traits under selection.

Gillman, M., Erenler, H., 2019. Reconciling the Earth's stratigraphic record with the structure of our galaxy. Geoscience Frontiers 10, 2147-2151.


The passage of our Solar System through the spiral arms has been implicated as a contributor to global environmental perturbations. The suggestion of a consistent structure within the arms, informed by density wave theory, raises the possibility of repeating patterns of events at each arm crossing. Here we test the hypothesis that the structure of the arms of our galaxy influences the stratigraphic record on Earth. We construct

independent structural and temporal models and combine these to compare the timings of arm tracers, materials from the earliest Solar System and events on Earth, including the largest extinctions. We find that a recurring sequence of events across the four arms emerges with an average arm-passing time of 188 million years. We suggest that the multiple temporal overlaps of events across arms, and their alignment with arm tracers and the earliest Solar System, presents an opportunity for a greater understanding of both Earth-based phenomena and galactic structure.

Gilmour, D.J., 2019. Microalgae for biofuel production. Advances in Applied Microbiology 109, 1-30.


Microalgae have been used commercially since the 1950s and 1960s, particularly in the Far East for human health foods and in the United States for wastewater treatment. Initial attempts to produce bulk chemicals such as biofuels from microalgae were not successful, despite commercially favorable conditions during the 1970s oil crisis. However, research initiatives at this time, many using extremophilic microalgae and cyanobacteria (e.g., Dunaliella and Spirulina), did solve many problems and clearly identified biomass productivity and harvesting as the two main constraints stopping microalgae producing bulk chemicals, such as biofuels, on a large scale. In response to the growing unease around global warming, induced by anthropogenic CO2 emissions, microalgae were again suggested as a carbon neutral process to produce biofuels. This recent phase of microalgae biofuels research can be thought to have started around 2007, when a very highly cited review by Chisti was published. Since 2007, a large body of scientific publications have appeared on all aspects of microalgae biotechnology, but with a clear emphasis on neutral lipid (triacylglycerol) synthesis and the use of neutral lipids as precursors for biodiesel production. In this review, the key research on microalgal biotechnology that took place prior to 2007 will be summarized and then the research trends post 2007 will be examined emphasizing the research into producing biodiesel from microalgae.

Gizatullin, B., Gafurov, M., Vakhin, A., Rodionov, A., Mamin, G., Orlinskii, S., Mattea, C., Stapf, S., 2019. Native vanadyl complexes in crude oil as polarizing agents for in situ proton dynamic nuclear polarization. Energy & Fuels 33, 10923-10932.


The presence of paramagnetic species such as vanadyl complexes (VO2+) and free carbon radicals in petroleum disperse systems (PDSs) such as crude oil, bitumen, or kerogen causes significant interest of studying the structure of PDS, high-molecular weight components, and their effects on the physical and chemical properties of PDS products by magnetic resonance techniques. However, the lack of detailed studies keeps the exact structure, aggregation mechanism, and interaction with complex composites of the PDS still disputable. In this contribution, detailed electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) investigations, including advanced fast field cycling dynamic nuclear polarization, of heavy crude oil focused on vanadyl complexes are presented. A perceptible room-temperature 1H dynamic nuclear polarization (DNP) solid effect at the X-band (magnetic field of 300–400 mT corresponding to the EPR frequency of 9.5 GHz and NMR frequency of 14.6 MHz), with enhancement ±5, is observed at moderate microwave irradiation power in crude oil with a high concentration of VO2+, while no Overhauser DNP contribution is found. Using NMR T2-encoding, DNP spectra and molecular dynamics, two components are distinguished, from which the one with slower dynamics exhibits higher DNP enhancement via VO2+ complexes. The observed difference is discussed in terms of electron–nuclear interaction and relative parts of hyperpolarized nuclear spins using an advanced model for DNP data simulation.

Gizzatov, A., Mashat, A., Kosynkin, D., Alhazza, N., Kmetz, A., Eichmann, S.L., Abdel-Fattah, A.I., 2019. Nanofluid of petroleum sulfonate nanocapsules for enhanced oil recovery in high-temperature and high-salinity reservoirs. Energy & Fuels 33, 11567-11573.


Petroleum sulfonate (PS) salt surfactants that are insoluble in high-salinity water were encapsulated into 10–60 nm oil swollen micelles dispersed by a cocamidopropyl hydroxysultaine zwitterionic cosurfactant to form a highly stable nanofluid at elevated salinity (∼56 000 mg/L) and temperature (∼100 °C). The resulting “Nano-Surfactant (NS)” fluid enables an economic, efficient, and environmentally friendly enhanced oil recovery (EOR) capable of targeted delivery of PS salt surfactants—one of the most abundant and inexpensive industrial surfactants, yet cannot be used in most EOR operations because of its insolubility in high-salinity water—to residual oil without the need of massive amounts of surfactants. The NS formulations presented here can be easily prepared in the field by a simple one-pot, one-step procedure at ambient temperatures and with a minimal energy input. This article reports the preparation method of the NS and results, demonstrating their long-term colloidal and chemical stability at 100 °C, reduction of crude oil–high-salinity water interfacial tension (IFT) by 3 orders of magnitude (from ∼10 to 0.008 mN/m), and improved mobilization of the trapped crude oil from the carbonate rock. Results point out the potential of NS formulations in enhancing oil mobilization under a variety of reservoir conditions. The NS platform described here can be utilized to encapsulate and deliver a variety of other chemical treatments, not only in oil recovery applications but also in others such as remediation of nonaqueous phase liquid-contaminated groundwater aquifers, well-drilling operations, and wellbore stimulation.

Glamoclija, M., Ramirez, S., Sirisena, K., Widanagamage, I., 2019. Subsurface microbial ecology at sediment-groundwater interface in sulfate-rich playa; White Sands National Monument, New Mexico. Frontiers in Microbiology 10, 2595. doi: 10.3389/fmicb.2019.02595.


The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.

Goldford, J.E., Hartman, H., Marsland, R., Segrè, D., 2019. Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. Nature Ecology & Evolution 3, 1715-1724.

https://doi.org/10.1038/s41559-019-1018-8

It has been suggested that a deep memory of early life is hidden in the architecture of metabolic networks, whose reactions could have been catalyzed by small molecules or minerals before genetically encoded enzymes. A major challenge in unravelling these early steps is assessing the plausibility of a connected, thermodynamically consistent proto-metabolism under different geochemical conditions, which are still surrounded by high uncertainty. Here we combine network-based algorithms with physico-chemical constraints on chemical reaction networks to systematically show how different combinations of parameters (temperature, pH, redox potential and availability of molecular precursors) could have affected the evolution of a proto-metabolism. Our analysis of possible trajectories indicates that a subset of boundary conditions converges to an

organo-sulfur-based proto-metabolic network fuelled by a thioester- and redox-driven variant of the reductive tricarboxylic acid cycle that is capable of producing lipids and keto acids. Surprisingly, environmental sources of fixed nitrogen and low-potential electron donors are not necessary for the earliest phases of biochemical evolution. We use one of these networks to build a steady-state dynamical metabolic model of a protocell, and find that different combinations of carbon sources and electron donors can support the continuous production of a minimal ancient ‘biomass’ composed of putative early biopolymers and fatty acids.

Golsefatan, A., Shahbazi, K., 2020. Predicting the effect of nanocomposites on asphaltene removal using a comprehensive approach. Petroleum Science and Technology 38, 64-73.

https://doi.org/10.1080/10916466.2019.1656241

Asphaltene precipitation is one of the major problems in petroleum industry that causes significant costs to the petroleum industry. Numerous researches have been done by researchers in order to mitigate, inhibit, or postpone these precipitates by using various inhibitors. Nanoparticles and nanocomposites have been applied to overcome this problem recently. In this study, a new model based on Least Square Support Vector Machine (LSSVM) approach is proposed to predict the effect of nanocomposites on asphaltene removal as a function of influencing parameters including nanocomposite type, temperature, pH, and the ratio of nanocomposite concentration to the initial asphaltene content (D/C0). Optimization process is done by Coupled Simulated Annealing (CSA) algorithm for tuning the developed model. Model accuracy is represented by calculating the statistical parameters. The predicted values by the model and actual data were in an excellent agreement with AARE, R2, and MSE values of 2.9431%, 0.9882, and 4.1511, respectively for overall data. Furthermore, sensitivity analysis was conducted on the input parameters which demonstrated that D/C0 and pH has the highest impact on asphaltene removal by nanocomposites and should be considered during process optimization.


https://doi.org/10.1017/S1473550418000538

Investigations into the existence of life in other parts of the cosmos find strong parallels with studies of the origin and evolution of life on our own planet. In this way, astrobiology and paleobiology are married by their common interest in disentangling the interconnections between life and the surrounding environment. In this way, a cross-point of both sciences is paleometry, which involves a myriad of imaging and geochemical techniques, usually non-destructive, applied to the investigation of the fossil record. In the last decades, paleometry has benefited from an unprecedented technological improvement, thus solving old questions and raising new ones. This advance has been paralleled by conceptual approaches and discoveries fuelled by technological evolution in astrobiological research. In this context, we present some new data and review recent advances on the employment of paleometry to investigations on paleobiology and astrobiology in Brazil in areas such biosignatures in Ediacaran microbial mats, biogenicity tests on enigmatic Ediacaran structures, research on Ediacaran metazoan biomineralization, fossil preservation in Cretaceous insects and fish, and finally the experimental study on the decay of fish to test the effect of distinct types of sediment on soft-tissue preservation, as well as the effects of early diagenesis on fish bone preservation.

Gong, D., Zhang, Y., Guo, W., Qi, R., Lu, S., Wu, W.a., 2019. Identification of secondary microbial methane and biodegradation: Case study from Luliang oil and gas field, Junggar Basin, China. Journal of Natural Gas Geoscience 4, 267-278.


The “secondary microbial gas” is defined as natural gas generated via the biodegradation of oil reservoirs. Since methane dominates, it is also called “secondary microbial methane”. Taking Luliang oil and gas field in the Junggar Basin as example, the methods for identifying secondary microbial methane and selective biodegradation of alkane gases were fully discussed in this study based on the molecular and stable carbon isotopes of natural gas as well as the geochemical characteristics of low molecular weight hydrocarbons of oil reservoirs. When the thermogenic gas is mixed with secondary microbial methane, its δ13C–CH4 ratio tends to be lighter with the C1/ƩC1–4 increasing. In the meantime, there is a tight relationship between secondary microbial methane, burial depth of gas reservoirs and the existence of biodegraded oil reserves. The methanogenesis is commonly accompanied by the selective biodegradation of C2–4 alkane gases, which results in the increasing of gas dry coefficients and the enrichment of 13C (even the reversal of carbon isotopes). Most currently used empirical diagrams to identify the gas genetic types are only applicable to the original thermogenic gases. All kinds of secondary alterations should be fully taken into consideration when these diagrams are used.

Gordadze, G.N., Giruts, M.V., Poshibaeva, A.R., Poshibaev, V.V., Gayanova, A.A., Postnikov, A.V., Postnikova, O.V., 2019. Study of the structure of benzene- and alcohol–benzene-extractable resins and kerogen of rock organic matter (by example of Bazhenovo Formation rocks from the north of the Gyda Peninsula). Petroleum Chemistry 59, 1177-1189.

https://doi.org/10.1134/S0965544119110045

Mild thermolysis of benzene- and alcohol–benzene-extracted resins and kerogen of the organic matter of Bazhenovo Formation rocks from the northern part of the Gyda Peninsula has been carried out. It has been revealed that macromolecular compounds of the benzene and alcohol–benzene resins and kerogen contain, as moieties, the homologous series of C10–C40n-alkanes, isoprenanes, C10–C30n-alkylcyclohexanes, and C10–C30n-alkylbenzenes; steranes; and terpanes found in crude oils. It has been shown that despite the difference in polarity of the benzene and alcohol–benzene resins, the relative distribution of hydrocarbon biomarkers in thermolysis products is close and differs from that in kerogen thermolysis products. The maturity of benzene and alcohol–benzene resins according to the sterane and terpane indexes is much lower than that of kerogen. As a result of the thermolysis of the resins of both types and kerogen, the unsaturated compounds isoprenene and squalene have been found, and oleanane was found in the thermolysis products of the alcohol–benzene resins. The pattern of distribution of n-alkanes and isoprenanes in the products of thermolysis of resins and kerogen is similar to that observed in the soluble part and in the thermolysates of Thermoplasma sp. archaea biomass in our previous study.

Grace, D.N., Sharp, J.R., Holappa, R.E., Lugos, E.N., Sebold, M.B., Griffith, D.R., Hendrickson, H.P., Galloway, M.M., 2019. Heterocyclic product formation in aqueous brown carbon systems. ACS Earth and Space Chemistry 3, 2472-2481.

https://doi.org/10.1021/acsearthspacechem.9b00235

Brown carbon in aerosol remains a significant source of error in global climate modeling due to its complex nature and limited product characterization. Though significant efforts have been made in the previous decade to identify the major light-absorbing brown carbon chromophores formed through the reactions of carbonyl-containing compounds with ammonium, substantial work is still required to identify the main absorbing species resulting from reactions of glyoxal, glycolaldehyde, and hydroxyacetone with ammonium sulfate (AS). Using tandem mass spectrometry and 15N experiments to confirm proposed structures and support their mechanistic pathways, compelling evidence is provided for the formation of pyrazines and imidazoles in the glyoxal + AS, glycolaldehyde + AS, and hydroxyacetone + AS systems. Through density functional theory calculations, the N-containing oligomers and aromatic heterocycles formed within these reaction systems are shown to contribute to brown carbon light absorption, thus holding significant relevance toward accurately predicting their effects on global climate.

Greenbaum, G., Getz, W.M., Rosenberg, N.A., Feldman, M.W., Hovers, E., Kolodny, O., 2019. Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nature Communications 10, 5003.

https://doi.org/10.1038/s41467-019-12862-7

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.

Griffiths, W.J., Wang, Y., 2019. Sterolomics in biology, biochemistry, medicine. TrAC Trends in Analytical Chemistry 120, 115280.


In mammalian systems “sterolomics” can be regarded as the quantitative or semi-quantitative profiling of all metabolites derived from cholesterol and its cyclic precursors. The system can be further complicated by metabolites derived from ingested phytosterols or pharmaceuticals, but this is beyond the scope of this article. “Sterolomics” can be performed on either an unbiased global format, or more usually, exploiting a targeted format. Here we discuss the different mass spectrometry-based analytical techniques used in “sterolomics” giving specific examples in the context of neurodegenerative disease and for the diagnosis of inborn errors of metabolism. We pay particular attention to the profiling of cholesterol metabolites in the bile acid biosynthesis pathways, although the analytical techniques discussed are also appropriate for analysis of hormonal steroids.

Grimmer, C., Rüger, C.P., Streibel, T., Cuoq, F., Kwakkenbos, G., Cordova, M., Peñalver, R., Zimmermann, R., 2019. Description of steam cracker fouling and coking residues by thermal analysis-photoionization mass spectrometry. Energy & Fuels 33, 11592-11602.


Two organic fouling samples obtained from downstream the cracking oven (DS) and from upstream the hot zone (US) of a steam cracker facility were characterized. For this purpose, a simultaneous thermal analyzer coupled to a photoionization mass spectrometer (STA-PI-MS) and a thermal desorption/pyrolysis gas chromatograph (TD/Py-GC-EI-MS) were used. Mass loss and differential scanning calorimetry information revealed the degradation of the materials beginning at 130 °C with two distinct maxima for US and one for DS (230–330 °C) as well as broad signals (330–500 °C) for both. Structural motives of different polymeric-like structures were assigned based on PI-MS of the effluent and separately conducted TD/Py-GC-EI-MS. The advantage of soft photoionization over hard ionization techniques such as electron ionization is the considerable reduction of fragmentation, yielding higher abundancies of molecular ions. Thus, even though complex samples are studied, evolving constituents can often be easily tracked in a time-resolved manner (1 Hz). While single photon ionization (SPI, 118 nm = 10.5 eV) ionizes most organic molecules, resonance-enhanced multiphoton ionization (REMPI, 2 × 266 nm = 9.4 eV) selectively addresses aromatic species. Differentiation of polymeric-like structures was achieved by exploiting this selectivity (SPI vs REMPI) and comparison of molecular patterns with GC-EI-MS data, which supports the identification of compounds by providing fragmentation patterns and chemical information based on retention time. US shows high inorganic content (∼50%) and more diversity in its organic part, as indicated by four types of patterns: polyethylene-like, Diels–Alder-like, polythioether/polysulfide-like, and polystyrene-like motives. In contrast, DS exhibits almost only signals of

Diels–Alder-like and polystyrene-like structures and contains a less inorganic material (∼23%). Additionally, first attempts to quantify the Diels–Alder content by STA-SPI-MS were successfully conducted.

Griscti, O., Camilleri, L., 2020. The impact of dog therapy on nursing students’ heart rates and ability to pay attention in class. International Journal of Educational Research 99, 101498.


In this study we explored if the presence of a therapy dog has an impact on students’ stress and ability to pay attention in class. The students' heart rates were measured when the dog was present and when he was absent. The students were also asked to fill in a questionnaire. results showed no significant difference in the students’ average and maximum heart rates, between the experimental and control group, however the average resting heart rate was lower when the dog was present. The low resting heart rate coupled with written comments from the students indicate that the presence of the dog did reduce stress and had a calming effect on the students.

Gröger, T.M., Käfer, U., Zimmermann, R., 2020. Gas chromatography in combination with fast high-resolution time-of-flight mass spectrometry: Technical overview and perspectives for data visualization. TrAC Trends in Analytical Chemistry 122, 115677.


Time-of-flight mass spectrometry combines fast acquisition speed with the ability to collect full spectral information and over the last years high mass resolution instrumentation become available for customers. These features make TOFMS very interesting for the hyphenation with fast or comprehensive two-dimensional gas chromatography. This publication reviews the technical progress of TOF-techniques with the focus on their compatibility with fast and ultra-fast chromatographic separations. A special focus is put on ionization techniques and data visualization approaches, covering related review article as well as selected primary literature and studies.



The rate of chemical weathering has been observed to increase with the rate of physical erosion in published comparisons of many catchments, but the mechanisms that couple these processes are not well understood. We investigated this question by examining the chemical weathering and porosity profiles from catchments developed on marine shale located in Pennsylvania, USA (Susquehanna Shale Hills Critical Zone Observatory, SSHCZO); California, USA (Eel River Critical Zone Observatory, ERCZO); and Taiwan (Fushan Experimental Forest). The protolith compositions, protolith porosities, and the depths of regolith at these sites are roughly similar while the catchments are characterized by large differences in erosion rate (1–3 mm yr−1 in Fushan ≫ 0.2–0.4 mm yr−1 in ERCZO ≫ 0.01–0.025 mm yr−1 in SSHCZO). The natural experiment did not totally isolate erosion as a variable: mean annual precipitation varied along the erosion gradient (4.2 m yr−1 in Fushan > 1.9 m yr−1 in ERCZO > 1.1 m yr−1 in SSHCZO), so the fastest eroding site experiences nearly twice the mean annual temperature of the other two.

Even though erosion rates varied by about 100×, the depth of pyrite and carbonate depletion (defined here as regolith thickness) is roughly the same, consistent with chemical weathering of those minerals keeping up with erosion at the three sites. These minerals were always observed to be the deepest to react, and they reacted until 100% depletion. In two of three of the catchments where borehole observations were available for ridges, these minerals weathered across narrow reaction fronts. On the other hand, for the rock-forming clay mineral chlorite, the depth interval of weathering was wide and the extent of depletion observed at the land surface decreased with increasing erosion/precipitation. Thus, chemical weathering of the clay did not keep pace with erosion rate.

But perhaps the biggest difference among the shales is that in the fast-eroding sites, microfractures account for 30–60% of the total porosity while in the slow-eroding shale, dissolution could be directly related to secondary porosity. We argue that the microfractures increase the influx of oxygen at depth and decrease the size of diffusion-limited internal domains of matrix, accelerating weathering of pyrite and carbonate under high erosion-rate conditions. Thus, microfracturing is a process that can couple physical erosion and chemical weathering in shales.



Although the cuticle is a very thin layer of a few micrometers, it is one of the main remains found among fossil plants. Apparently very fragile, ultrathin cuticle sections of few dozen nanometers thick are studied by using TEM studies and statistical measurements. The ultrastructure details yielded are of significance not only for taxonomy, but also for paleoenvironment and evolution of fossil plant. After an historical introduction and a review of the methods to obtain and observe the ultrathin sections, although data are still not enough numerous, detailed information and interesting facts of cuticle ultrastructure emerge from the studied plant groups. This paper gives a review of the main results of transmission electron microscopy -TEM- of fossil plant cuticles since the pioneering study 33 years ago.

Guillemot, T., Stockhecke, M., Bechtel, A., Ladd, S.N., Nelson, D.B., Schubert, C.J., 2019. Paleoenvironmental and paleoclimatic variations around Lake Van (Eastern Turkey) recorded by sedimentary source specific biomarkers 250–130 ka (MIS7 and MIS6). Quaternary Science Reviews 225, 105997.


Paleoclimatic changes during MIS7 and MIS6 remain poorly described in the Near East. We quantified source-specific biomarkers in Lake Van sediments during the interglacial/glacial cycle MIS7/MIS6. Long-chain n-alkanes produced by land-derived vegetation, as well as long-chain alkenones and sterols (namely brassicasterol and dinosterol) produced by aquatic algae were investigated. Stable hydrogen isotopic measurements (δ2H) on n-C29 alkanes were used as a proxy for aridity and revealed three wetter periods interrupted by two drier intervals during MIS7. In contrast, during the MIS6 glaciation, a generally drier climate was predominant. During the warmer and wetter periods of MIS7, a higher input of aquatic organic matter to Lake Van sediments was recorded by higher concentrations of long-chain alkenones, dinosterol and brassicasterol. Long-chain alkane abundances do not show a pattern related to aridity and were observed in higher concentrations in wetter as well as drier periods. Generally, in the Eastern Mediterranean, a wetter interglacial interrupted by drier episodes followed by a dry glacial period was the common feature observed during the MIS7/MIS6 interglacial/glacial cycle. However, in comparison to the last interglacial/glacial cycle the extreme dry glacial period registered around Lake Van from MIS5d to MIS2 was apparently unique and not equaled by a similar event within the last 250 ka.



Physical properties like porosity and density are important parameters for size estimations of fossil fuel reservoir in host sediments and rocks. X-ray CT based imaging and subsequent analysis of the images by using various techniques for estimations of these properties of host rocks and sediments has been attempted. However, most of those techniques tend to be biased and subjective due to complications in image processing. Here we describe a new procedure for estimating porosity and density without processing the XCT images, but

using the raw data that are used for producing the images. In this study, large-size cylindrical core samples (up to 150 cm long and 6.6 cm diameter) were imaged in a matter of minutes by using a medical XCT scanner soon after their recovery from seafloor onboard drillship in order to record as realistic as possible condition of hydrate-bearing sediments. Despite some uncertainty in relative volumes of solid, liquid and gas phases at voxel level, the results obtained by this rapid and non-destructive procedure are in good agreement with those obtained by time- and sample-consuming conventional methods of physical property measurements.



To better understand evolution of oil-prone sedimentary organic matter to petroleum and expulsion from source rock, we evaluated organic petrographic features of Leonardian Wolfcamp A repetitive siliceous and calcareous mudrock and fine-grained carbonate lithofacies cycles occurring in the R. Ricker #1 core from Reagan County, Midland Basin, Texas. The objectives of the petrographic investigation were to estimate thermal maturity, identify organic matter types and abundances, and identify the presence or absence of migrated hydrocarbons in organic-lean carbonate layers. An integrated analytical program included geochemical screening [total organic carbon (TOC) content by LECO, programmed pyrolysis by hydrocarbon analyzer with kinetics (HAWK) including analysis of solvent-extracted samples], X-ray diffraction mineralogy, organic petrography, scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS) including correlative light and electron microscopy (CLEM), and micro-Fourier transform infrared spectroscopy (μ-FTIR) analyses of solid bitumen. The data indicate all samples are early to middle oil window thermal maturity with solid bitumen reflectance (BRo) values of 0.55–0.86% and Tmax of 440–455 °C. Organic matter is predominantly solid bitumen (as identified by optical microscopy) in all lithofacies with minor contributions from inertinite. Solid bitumen abundance decreases from siliceous mudrock (TOC >3.0 wt%) to calcareous mudrock (TOC 1.0 to 3.0 wt%) to fine-grained carbonate (TOC <1.0 wt%) lithofacies. Interpretations of petrographic data suggest siliceous and calcareous mudrocks are source rock lithofacies and contain solid bitumen (with petroleum generation potential) that is residual (what remains) from conversion of an original Type II sedimentary organic matter. In turn, fine-grained carbonates are interpreted as reservoir lithofacies which contained little or no original oil-prone sedimentary organic matter and at present-day contain only a minor component of migrated solid petroleum sourced from adjacent siliceous and calcareous mudrock lithofacies. This work helps to document petroleum generation and migration processes, improve unconventional reservoir characterization and better define areas of oil window thermal maturity in an area critical to United States hydrocarbon production.

Haezeleer, B., Böttger, U., de Vera, J.-P., Hanke, F., Fox, S., Strasdeit, H., 2019. Artifact formation during Raman measurements and its relevance to the search for chemical biosignatures on Mars. Planetary and Space Science 179, 104714.


Raman spectroscopy will be a powerful tool in the in situ search for Martian biosignatures within the ESA/Roscosmos ExoMars and NASA Mars 2020 missions. However, a Raman laser can alter the chemical nature of a sample. This prompted us to investigate the stability of potential biosignatures during Raman measurements. For our study, we selected the photosynthetic pigment β-carotene, the biological membrane component 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), the iron porphyrin hemin, and the electron transfer protein cytochrome c. The excitation wavelength was 532 nm, which is the wavelength at which the lasers of the RLS (ExoMars) and SuperCam (Mars 2020) instruments will operate. We found that β-carotene and DOPE were stable up to 7.0 mW, which was the maximum laser power in our experiments, corresponding to an irradiance of 378 kW/cm2. Hemin and cytochrome c, by contrast, decomposed when the energy input exceeded a certain threshold. For example, hemin started to decompose in the 0.05–0.8 mW range (2.5–40 kW/cm2) under Mars-like conditions (200 K, vacuum, 50 s total irradiation time). Carbonaceous materials were the final decomposition products of both compounds. Our experiments also showed that low

temperatures near the average Martian surface temperature of ~210 K can delay the decomposition of biomolecules. In addition to loose powders, we studied thin layers pressed on NaCl pellets, where NaCl served as a model mineral matrix. In the case of hemin and cytochrome c on NaCl, the measurements could be performed with higher laser powers because of more efficient heat dissipation by the salt. For comparison, spectra were also recorded under standard laboratory conditions, i.e., at room temperature and atmospheric pressure. A major conclusion of this work is that Raman lasers used on Mars may alter biomolecules by heating the sample and, in specific cases, transform them into carbonaceous matter. The resulting spectra may be misinterpreted as evidence of extinct rather than extant life or even as evidence of non-biological material.


https://doi.org/10.1038/s41396-019-0485-x

The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.

Hale, O.J., Cramer, R., 2019. Atmospheric pressure ultraviolet laser desorption and ionization from liquid samples for native mass spectrometry. Analytical Chemistry 91, 14192-14197.


Understanding protein structure is vital for evaluating protein interactions with drugs, proteins, and other ligands. Native mass spectrometry (MS) is proving to be invaluable for this purpose, enabling analysis of “native-like” samples that mimic physiological conditions. Native MS is usually performed by electrospray ionization (ESI) with its soft ionization processes and the generation of multiply charged ions proving favorable for conformation retention and high mass analysis, respectively. There is scope to expand the currently available toolset, specifically to other soft ionization techniques such as soft laser desorption, for applications in areas like high-throughput screening and MS imaging. In this Letter, observations made from native MS experiments using an ultraviolet (UV) laser-based ion source operating at atmospheric pressure are described. The ion source is capable of producing predominately multiply charged ions similar to ESI. Proteins and protein complexes were analyzed from a native-like sample droplet to investigate the technique. Ion mobility-mass spectrometry (IM-MS) measurements showed that folded protein conformations were detected for ions with low charge states. This observation indicates the source is suitable for native MS analysis and should be further developed for higher mass analysis in the future.

Hallek, T., Akrout, D., Ahmadi, R., Montacer, M., 2020. Assessment of sedimentary environment from PAHs and aliphatic biomarkers: The case study of Fahdene black shales in northern Tunisia. Journal of African Earth Sciences 161, 103676.


Polyaromatic and aliphatic biomarkers extracted from the Albian-Early Cenomanian source rock (Fahdene Formation) were evaluated by Gas Chromatography – Mass Spectrometry (GC-MS) and are compared to classic geochemical and mineralogical data. In addition to terpanes, hopanes, diasteranes and steranes, thirty-seven aromatic hydrocarbon elements were identified.

The absence of the angiosperm-derived biomarker (18α(H)-Oleanane) and the low abundance of trimethylnaphthalenes isomers (1,2,5-TMN and 1,2,7-TMN) suggest that no land-plant traces were founded in the studied organic matter. In this fact, the Kerogene III identified by Rock Eval is not detected, and we can attribute these indices to the algae effect. The check of maturity by Tmax and the biomarker parameters (C27 18α-22,29,30-trinorneohopane (Ts), sterane isomerization ratio ββ/(αα+ββ), C32 22S/(22S + 22R) HH and the methylphenanthrene index (MPI-1)) indicates that these organic rich sediments are reached the early stage of oil window. In the other hand, aliphatic and polyaromatic biomarkers confirm classic data of X-ray diffraction and calcimetry and suggest a carbonate facies with some clayey intercalations in the middle part. The fracturing analysis of these carbonates prove the presence of high density of fractures with various sizes and directions. About filling, the fibrous calcite is the major element of mineralized veins, with the presence of bitumen traces. These fractures have two main orgin; the fluid pressure and the regional tectonic stress regime.

Therefore, the Albian-Early Cenomanian fractured carbonates in the Mahjouba area were deposited, under suboxic conditions, in a marine environment affected by the eutrophication phenomenon, and have just reached the equilibrium stage of maturity.

Hallsworth, J.E., 2019. Microbial unknowns at the saline limits for life. Nature Ecology & Evolution 3, 1503-1504.

https://doi.org/10.1038/s41559-019-1021-0

The pools of the geothermal Dallol Dome and surrounding area (in the Danakil Depression of Ethiopia) are an extreme example of complex brines: many lack evidence of life, but others are habitats for archaea and other extremophiles, prompting questions about the biophysical limits for microbial function.

Hamada, Y., Hirose, T., Saito, S., Moe, K., Wu, H., Tanikawa, W., Sanada, Y., Nakamura, Y., Shimmoto, Y., Sugihara, T., Lin, W., Abe, N., Gupta, L., Kinoshita, M., Masaki, Y., Nomura, S., Yamada, Y., 2019. Equivalent formation strength as a proxy tool for exploring for the location and distribution of gas hydrates. Marine and Petroleum Geology 108, 356-367.


Gas hydrate-bearing layers are normally identified by a seismic imaged bottom simulating reflectors (BSR) or by downhole log responses because of their high acoustic velocity and electric resistivity compared to surrounding formations. These gas hydrate characteristics can also result in contrasting in-situ formation compressive strengths. Here, we describe gas hydrate-bearing layers based on equivalent strength (EST), which relates to in-situ compressive strength, in five exploration boreholes drilled during the Indian National Gas Hydrate Program Expedition 02 (NGHP-02). For Site NGHP-02-23, a representative site for those that were established during NGHP-02, the EST evaluated from drilling parameters shows a constant trend of ∼2 MPa, with some strong peak values in the 0–271.4 m-below-seafloor (mbsf) interval, and a sudden increase up to 4 MPa above the BSR depth (271.4–290.0 mbsf). Below the BSR, the EST stays at ∼2 MPa to the bottom of the hole (378 mbsf). Comparing the EST with logging data and a core sample description suggests that the EST depth profiles reflect the formation lithology and gas hydrate content. The EST increases in sand-rich and gas hydrate-bearing zone. In the lower gas hydrate layers in particular, the EST curve shows the same approximate trend with that of P-wave velocity and resistivity measured during downhole logging. Similar relationships

between EST, hydrate layer, and log responses are confirmed in other four sites drilled nearby in NGHP-02 Area B. These results suggest that the EST, as a proxy for in-situ formation strength, can indicate the location and extent of the gas hydrate as well as borehole logging. Although the EST was calculated after drilling, utilizing the recorded surface drilling parameters (weight on bit, top drive torque, RPM and rate of penetration) in this study, the EST can be acquired during drilling using real-time drilling parameters. In addition, the EST only requires drilling performance data without any additional tools or measurements, making it a simple and economical tool for the exploration of gas hydrates.



Deep-sea dissolved organic matter (DOM) constitutes a huge carbon reservoir in the worlds' oceans that – despite its abundance – is virtually unused as a substrate by marine heterotrophs. Heating within hydrothermal systems induces major molecular modifications of deep-sea DOM. Here, we tested the hypothesis that hydrothermal heating of deep-sea DOM enhances bioavailability. Aliquots of DOM extracted from the deep North Pacific (North Equatorial Pacific Intermediate Water; NEqPIW) were re-dissolved in artificial seawater and subjected to temperatures of 100 and 200 °C (40 MPa) using Dickson-type reactors. In agreement with earlier findings we observed a temperature-related drop in dissolved organic carbon (DOC) concentration (−6.1% at 100 °C, −21.0% at 200 °C) that predominantly affected the solid-phase extractable (SPE-DOC) fraction (−18.2% at 100 °C, −51.4% at 200 °C). Fourier-transform ion cyclotron resonance mass spectrometric (FT-ICR-MS) analysis confirmed a temperature-related reduction of average molecular mass, O/C ratios, double bond equivalents (DBE) and a relative increase in aromaticity (AImod). This thermally altered DOM was added (25 μmol L−1 DOC) to deep-water samples from the South West Pacific (Kermadec Arc, RV Sonne / SO253, 32° 37.706′ S | 179° 38.728′ W) and incubated with the prevailing natural microbial community. After 16 days at 4 °C in the dark, prokaryotic cell counts in incubations containing the full spectrum of thermally-degraded DOM (extractable and non-extractable compounds) had increased considerably (on average 21× for DOM100°C and 27× for DOM200°C). In contrast, prokaryotic growth in incubations to which only solid-phase extractable thermally-altered DOM was added was not enhanced compared to control incubations. The experiments demonstrate that temperature-driven degradation of deep-sea recalcitrant DOM within hydrothermal systems turns fractions of it accessible to microbes. The thermally-produced DOM compounds that stimulate microbial growth are not retained on reversed-phase resins (SPE-DOM) and are likely low-molecular mass organic acids. Despite the comprehensive compositional modifications of the solid-phase extractable (SPE-DOM) fraction through heating, it remains inaccessible to microbes at the investigated concentration levels. The microbial incubation resulted in only minor and mostly insignificant overall changes in SPE-DOM molecular composition and concentration.

Hanson, J.R., Nichols, T., Mukhrish, Y., Bagley, M.C., 2019. Diterpenoids of terrestrial origin. Natural Product Reports 36, 1499-1512.

http://dx.doi.org/10.1039/C8NP00079D

Covering January to December 2017; previous review Nat. Prod. Rep., 2017, 34, 1233–1243. This review covers the isolation and chemistry of diterpenoids from terrestrial as opposed to marine sources and includes labdanes, clerodanes, abietanes, pimaranes, kauranes, cembranes and their cyclization products. There are 228 references.

Hardy, K., 2019. Paleomedicine and the use of plant secondary compounds in the Paleolithic and Early Neolithic. Evolutionary Anthropology: Issues, News, and Reviews 28, 60-71.

https://doi.org/10.1002/evan.21763

Abstract Reconstructing plant use before domestication is challenging due to a lack of evidence. Yet, on the small number of sites with assemblages, the wide range of different plant species cannot be explained simply in terms of nutrition. Assemblages from the Lower Paleolithic to the Early Neolithic were examined to investigate the relative edible and medicinal properties of the plants. The assemblages contain a mixture of edible species, plants that are both edible and medicinal, and plants with only medicinal properties. The proportion of medicinal plants at all sites is well above the natural average and increases over time. Mechanisms for preventing intestinal parasitic infections are common among animals and together with chimpanzees? preventative and curative self-medication practices suggest an evolutionary context for this behavior. A broad-spectrum approach to plant collection is likely to have been in place throughout the Paleolithic driven, in part, by the need for medicinal compounds.


https://doi.org/10.1029/2018JG004997

Abstract: Substantial changes in vegetation are expected as global climatic patterns shift, altering terrestrial sources of dissolved organic matter (DOM) entering rivers and streams. Since differences in the chemical composition of plant litters are reflected in the DOM that is leached, changes in riparian vegetation can directly influence the bioavailability of DOM to local aquatic microbial communities. We assessed the degradation dynamics and optical compositional changes of DOM from a variety of vascular plant leachates through microbial and coupled photochemical‐microbial degradation pathways. Initial decay rates ranged from 0.029 ± 0.011 day−1 (microbial, mixed wetland) to 0.73 ± 0.62 day−1 (photochemical‐microbial, mixed grasses), and all decay rates decreased to below 0.05 day−1 after 1 week, converging below 0.029 day−1 after 2 weeks. Overall, we found a decrease in leachate optical diversity under microbial and photochemical‐microbial degradations, corresponding to a decrease in degraded leachate sample dispersion using principal component analysis. We show that despite initial variability across DOM leachates, successive degradation promotes kinetic and optical convergence such that, in aquatic environments with long residence times, terrestrial DOM source and composition are much less important on exported DOM composition than historically thought. In these systems, DOM compositional convergence may act as a natural buffer to provide stability of aquatic DOM cycling in the face of future landscape changes.

Plain Language Summary: Future changes in climate are expected to affect where and when plants will grow. By the year 2100, for example, native California oak trees may occupy only half their current land area and likely will grow only at higher latitudes, causing concern for organisms that depend on native oak trees for food. When leaves fall into water, they break down into small pieces that become part of the dissolved organic matter in aquatic systems. Dissolved organic matter provides food for aquatic bacteria, and these bacteria become food for zooplankton and fish. Since each plant species has its own chemical fingerprint, some dissolved organic matter is more difficult to degrade. Thus, if a plant like the California oak tree disappeared from its current geographic area, bacteria might not have another easily degradable food source. However, we found that after being processed (through partial degradation by bacteria or exposure to sunlight), dissolved organic matter loses its distinct chemical fingerprint and is equally accessible to bacteria regardless of the plant from which it came. This uniformity acts as a buffer to the food web against shifts in plant species since bacteria can switch to different plant species if their current food source disappears.

Harper, D.A.T., Hammarlund, E.U., Topper, T.P., Nielsen, A.T., Rasmussen, J.A., Park, T.-Y.S., Smith, M.P., 2019. The Sirius Passet Lagerstätte of North Greenland: a remote window on the Cambrian Explosion. Journal of the Geological Society 176, 1023.


The lower Cambrian Lagerstätte of Sirius Passet, Peary Land, North Greenland, is one of the oldest of the Phanerozoic exceptionally preserved biotas. The Lagerstätte evidences the escalation of numbers of new body plans and life modes that formed the basis for a modern, functionally tiered ecosystem. The fauna is dominated

by predators, infaunal, benthic and pelagic, and the presence of abundant nekton, including large sweep-net feeders, suggests an ecosystem rich in nutrients. Recent discoveries have helped reconstruct digestive systems and their contents, muscle fibres, and visual and nervous systems for a number of taxa. New collections have confirmed the complex combination of taphonomic pathways associated with the biota and its potentially substantial biodiversity. These complex animal-based communities within the Buen Formation were associated with microbial matgrounds, now preserved in black mudstones deposited below storm wave base that provide insight into the shift from late Neoproterozoic (Ediacaran) to Cambrian substrates and communities. Moreover, the encasing sediment holds important data on the palaeoenvironment and the water-column chemistry, suggesting that these animal-based communities developed in conditions with very low oxygen concentrations.


https://doi.org/10.1098/rspb.2019.1409

Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.


https://doi.org/10.1038/s41598-019-52745-x

Large hydrate reservoirs in the Arctic regions could provide great potentials for recovery of methane and geological storage of CO2. In this study, injection of flue gas into permafrost gas hydrates reservoirs has been studied in order to evaluate its use in energy recovery and CO2 sequestration based on the premise that it could significantly lower costs relative to other technologies available today. We have carried out a series of real-time scale experiments under realistic conditions at temperatures between 261.2 and 284.2 K and at optimum pressures defined in our previous work, in order to characterize the kinetics of the process and evaluate efficiency. Results show that the kinetics of methane release from methane hydrate and CO2 extracted from flue gas strongly depend on hydrate reservoir temperatures. The experiment at 261.2 K yielded a capture of 81.9% CO2 present in the injected flue gas, and an increase in the CH4 concentration in the gas phase up to 60.7 mol%, 93.3 mol%, and 98.2 mol% at optimum pressures, after depressurizing the system to dissociate CH4 hydrate and after depressurizing the system to CO2 hydrate dissociation point, respectively. This is significantly better than the maximum efficiency reported in the literature for both CO2 sequestration and methane recovery using flue gas injection, demonstrating the economic feasibility of direct injection flue gas into hydrate reservoirs in permafrost for methane recovery and geological capture and storage of CO2. Finally, the thermal stability of stored CO2 was investigated by heating the system and it is concluded that presence of N2 in the injection gas provides another safety factor for the stored CO2 in case of temperature change.

Hazra, B., Chandra, D., Singh, A.K., Varma, A.K., Mani, D., Singh, P.K., Boral, P., Buragohain, J., 2019. Comparative pore structural attributes and fractal dimensions of Lower Permian organic-matter-bearing sediments of two Indian basins: Inferences from nitrogen gas adsorption. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 2975-2988.

https://doi.org/10.1080/15567036.2019.1582737

Pore structural framework of Lower Permian shales from two Indian basins is investigated using a low-pressure nitrogen adsorption–desorption technique. Specific surface areas (SSA) of shales are controlled by their thermal maturity. Thermally mature shales are marked by lower average pore sizes, diminishing pore size distribution style from the finer to the coarser pores, and higher fractal dimension D2, relative to the less mature shales. D2 (pore structural fractal dimension) showed a positive relationship with SSA and maturity and a negative correlation with pore sizes. The fractal-distinguishing parameter ∆S was higher for the mature shales. With increasing maturities, pore structures become complex and the fractal dimensions become more distinct.

He, L., Mei, H., Hu, X., Dejam, M., Kou, Z., Zhang, M., 2019. Advanced flowing material balance to determine original gas in place of shale gas considering adsorption hysteresis. SPE Reservoir Evaluation & Engineering 22, 1282-1292.

https://doi.org/10.2118/195581-PA

A series of shale gas adsorption and desorption experiments are conducted. Desorption and adsorption curves are not coincident, with the former located above the latter, which suggests that adsorption hysteresis also occurs in shale gas. Pseudodeviation factor (Z*) is revised to advance the material-balance equation (MBE) and flowing material balance (FMB). The case study of the Fuling Shale in China illustrates that original gas in place (OGIP) of all three wells (1-HF, 2-HF, and 3-HF) calculated by conventional FMB is lower than that calculated by refined FMB, which has accounted for adsorption hysteresis. The conventional FMB underestimates OGIP of the three wells by 2.21, 3.29, and 4.02%, respectively. Adsorption hysteresis should be accounted for to accurately determine OGIP.


https://doi.org/10.1038/s41598-019-52661-0

Pseudomonas sp. strain NEE2 isolated from oil-polluted soils could biodegrade n-hexane effectively. In this study, the secretory product of n-hexane biodegradation by NEE2 was extracted, characterized, and investigated on the secretory product’s enhanced effect on n-hexane removal. The effects of various biodegradation conditions on n-hexane removal by NEE2, including nitrogen source, pH value, and temperature were also investigated. Results showed that the secretory product lowered surface tension of water from 72 to 40 mN/m, with a critical micelle concentration of 340 mg/L, demonstrating that there existed biosurfactants in the secretory product. The secretory product at 50 mg/L enhanced n-hexane removal by 144.4% within 48 h than the control group. The optimum conditions for n-hexane removal by NEE2 were at temperature of 25–30 °C, pH value of 7–8, and (NH4)2SO4 as nitrogen source. Besides n-hexane, NEE2 could also utilize a variety of carbon sources. These results proved that NEE2 can consume hydrophobic volatile organic compounds (VOCs) to produce biosurfactants which can further enhance hydrophobic VOCs degradation.



The presence of surfactants in biofilters could enhance hydrophobic VOC removal. In this study, blood agar plate, methylene blue agar plate and a culture with n-hexane as the only carbon source were used to screen strains that could biodegrade n-hexane and produce biosurfactants simultaneously. The effects of n-hexane concentration on n-hexane removal and biosurfactant production were also investigated. Results showed that such a strain identified to be Pseudomonas sp. Strain NEE2 was successfully isolated from oil-polluted soils. The biosurfactants production by this strain were dependent on the initial concentration of n-hexane (132–

2640 mg/L). At the concentration of 2640 mg/L of n-hexane, the biosurfactants promoted n-hexane removal. At 132 mg/L of n-hexane, n-hexane removal efficiency on day 2 exceeded 60%. The synergistic mechanisms of n-hexane removal and biosurfactant production by Pseudomonas sp. Strain NEE2 were discussed including the enhanced mass transfer from gas to liquid phase, within the biofilm phase and biodegradation at the presence of biosurfactants as well as the consequently enhanced production of the biosurfactants. These results in this study proved that it is possible for microorganisms utilizing the synergistic effect of hydrophobic VOC degradation and biosurfactant production for cost-effective hydrophobic VOC removal in biofilters.

He, S., Tan, J., Hu, W., Mo, C., 2019. Diversity of archaea and its correlation with environmental factors in the Ebinur Lake wetland. Current Microbiology 76, 1417-1424.

https://doi.org/10.1007/s00284-019-01768-8

The diversity and community composition of archaea in soil samples from three wetlands (SP1, SP2, and SP3) of Ebinur Lake were studied by constructing 16S rDNA cloning library. The correlation between the diversity of archaea and soil environmental factors was analyzed by CANOCO software. The aim of this study was to reveal the differences of community structures of archaea in different sample sites, to provide a theoretical basis for further study on degradation and restoration of Ebinur Lake wetland. The results showed that Euryarchaeota accounted for 57.1% was the most dominant phylum observed, followed by Thaumarchaeota and Crenarchaeota for the three wetland soil analyzed. Compared with SP3 site, the proportions of Euryarchaeota were decreased by 16.70% and 31.78%, while Thaumarchaeota increased by 7.26% and 17.64% in the SP1 and SP2, respectively. Crenarchaeota was found only in SP3. Shannon–wiener diversity indices in SP1, SP2, and SP3 sites were 3.44, 3.87, and 3.94, respectively, indicating that the diversity of archaea in three plots was: SP3 > SP2 > SP1. Redundancy analysis (RDA) showed that electrical conductivity (EC), soil moisture (SM), hydrogen potential (pH), and soil organic matter content (SOM) may affect archaeal communities. Compared to EC and pH, SM and SOM may have a greater impact on the community composition of archaea.

He, W., Guo, J., Guo, H., An, M., Huang, W., Wang, Y., Cai, H., 2019. Sphingobacterium puteale sp. nov., isolated from a deep subsurface aquifer. International Journal of Systematic and Evolutionary Microbiology 69, 3356-3361.

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003521

A bacterial strain M05W1-28T was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped, non-motile, aerobic, stained Gram-negative. Optimal growth was obtained at pH 7.0 (range: 6.0–9.0), 28 °C (range: 15–37 °C) and 0 % NaCl (range: 0–1.5 %, w/v) in modified tryptic soy broth (mTSB) without added NaCl and R2A. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c) and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, glycolipid, phosphoglycolipids, phospholipids, and unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The genomic G+C content of strain M05W1-28T was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28T was affiliated with the genus Sphingobacterium , exhibiting the highest sequence similarities with S. multivorum LMG 8342T (97.5 %), S. ginsenosidimutans THG07T (97.1 %) and less than 97.0 % to other members of the genus. The average nucleotide identity (ANI) and digital DNA–DNA hybridisation values (dDDH) between M05W1-28T and S. multivorum LMG 8342T were 78.1 and 22.5 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilisation differentiated the strain from other Sphingobacterium species. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain M05W1-28T represented a novel species within the genus Sphingobacterium , for which the name Sphingobacterium puteale sp. nov. is proposed. The type strain is M05W1-28T (=CGMCC 1.13711T=KCTC 72027T).

He, Y., Bao, H., Liu, Y., 2020. Predicting equilibrium intramolecular isotope distribution within a large organic molecule by the cutoff calculation. Geochimica et Cosmochimica Acta 269, 292-302.


A predicted equilibrium intramolecular isotope distribution (Intra-ID) serves as a reference for measured position-specific (PS) isotope composition variation in an organic molecule. Equilibrium Intra-ID can be estimated from calculated reduced partition function ratios (RPFR or β factor), which are largely absent to date. For relatively small molecules, the PS β factor can be calculated directly. However, estimating the PS β factor considering an entire, large organic molecule is computationally prohibitive. The isotope effect is local in that the vibrational frequencies of an atom are only affected by its proximal bonding environment. Therefore, the cutoff calculation, which simplifies the calculation of an entire molecule to a local area, was previously proposed for large organic molecules. However, the cutoff size was not validated, which has hindered the application of the cutoff calculation. Here, we calculated a series of small organic molecules with 2–18 carbon atoms to test the influence of cutoff size on the 13β value estimation of a target carbon position in a carbon chain or a carbon ring. We calculated nineteen small molecules that have a methyl carbon and a functional group that is at least three bonds away from the target methyl position. The result showed that the equilibrium 13C enrichment of the methyl group relative to CO2 at 25 °C (ln13α(eq)) for the nineteen molecules varied in a small range, with a standard deviation of 0.2‰. Fourteen aromatic hydrocarbons with a benzene and one adjacent functional group were calculated to test the influence of different adjacent functional groups on similar carbon positions in benzene. The results showed that different adjacent functional groups had significant influence only on the predicted ln13α(eq) value of the carbon position directly connected to them (standard deviation = 1.0‰, n = 14), with a negligible influence on the predicted ln13α(eq) value of the remaining carbons in benzene (standard deviation = 0.2‰, n = 14). The PS 13β value of a specific carbon position in CoA calculated by the cutoff calculation differed from that of the entire-molecule calculation by 0.0–0.3‰. We concluded that the cutoff calculation simplified the calculation of a target position from an entire molecule to a cluster of three proximal bonds in a chain and/ or an adjacent ring, providing PS 13β values of sufficient accuracy for large organic molecules.

Henehan, M.J., Ridgwell, A., Thomas, E., Zhang, S., Alegret, L., Schmidt, D.N., Rae, J.W.B., Witts, J.D., Landman, N.H., Greene, S.E., Huber, B.T., Super, J.R., Planavsky, N.J., Hull, P.M., 2019. Rapid ocean acidification and protracted Earth system recovery followed the end-Cretaceous Chicxulub impact. Proceedings of the National Academy of Sciences 116, 22500-22504.


Significance: Debate lingers over what caused the last mass extinction 66 million years ago, with intense volcanism and extraterrestrial impact the most widely supported hypotheses. However, without empirical evidence for either’s exact environmental effects, it is difficult to discern which was most important in driving extinction. It is also unclear why recovery of biodiversity and carbon cycling in the oceans was so slow after an apparently sudden extinction event. In this paper, we show (using boron isotopes and Earth system modeling) that the impact caused rapid ocean acidification, and that the resulting ecological collapse in the oceans had long-lasting effects for global carbon cycling and climate. Our data suggest that impact, not volcanism, was key in driving end-Cretaceous mass extinction.

Abstract: Mass extinction at the Cretaceous–Paleogene (K-Pg) boundary coincides with the Chicxulub bolide impact and also falls within the broader time frame of Deccan trap emplacement. Critically, though, empirical evidence as to how either of these factors could have driven observed extinction patterns and carbon cycle perturbations is still lacking. Here, using boron isotopes in foraminifera, we document a geologically rapid surface-ocean pH drop following the Chicxulub impact, supporting impact-induced ocean acidification as a mechanism for ecological collapse in the marine realm. Subsequently, surface water pH rebounded sharply with the extinction of marine calcifiers and the associated imbalance in the global carbon cycle. Our reconstructed water-column pH gradients, combined with Earth system modeling, indicate that a partial ∼50% reduction in global marine primary productivity is sufficient to explain observed marine carbon isotope patterns at the K-Pg, due to the underlying action of the solubility pump. While primary productivity recovered within a few tens of thousands of years, inefficiency in carbon export to the deep sea lasted much longer. This phased recovery scenario reconciles competing hypotheses previously put forward to explain the K-Pg carbon isotope records, and explains both spatially variable patterns of change in marine productivity across the event and a lack of

extinction at the deep sea floor. In sum, we provide insights into the drivers of the last mass extinction, the recovery of marine carbon cycling in a postextinction world, and the way in which marine life imprints its isotopic signal onto the geological record.

Hepp, J., Glaser, B., Juchelka, D., Mayr, C., Rozanski, K., Schäfer, I.K., Stichler, W., Tuthorn, M., Zech, R., Zech, M., 2019. Validation of a coupled δ2Hn-alkane-δ18Osugar paleohygrometer approach based on a climate chamber experiment. Biogeosciences Discussions 2019, 1-30.

https://www.biogeosciences-discuss.net/bg-2019-427/

The hydrogen isotopic composition of leaf wax-derived biomarkers, e.g. long chain n-alkanes (δ2Hn-alkane), is widely applied in paleoclimatology research. However, a direct reconstruction of the isotopic composition of paleoprecipitation based on δ2Hn-alkane alone can be challenging due to the overprint of the source water isotopic signal by leaf-water enrichment. The coupling of δ2Hn-alkane with δ18O of hemicellulose-derived sugars (δ18Osugar) has the potential to disentangle this effect and additionally allow relative humidity reconstructions. Here, we present δ2Hn-alkane as well as δ18Osugar results obtained from leaves of the plant species Eucalyptus globulus, Vicia faba var. minor and Brassica oleracea var. medullosa, which were grown under controlled conditions. We addressed the questions (i) do δ2Hn-alkane and δ18Osugar values allow precise reconstructions of leaf water isotope composition, (ii) how accurately does the reconstructed leaf-water-isotope composition enables relative humidity (RH) reconstruction in which the plants grew, and (iii) does the coupling of δ2Hn-alkane and δ18Osugar enable a robust source water calculation?

For all investigated species, the alkane n-C29 was most abundant and therefore used for compound-specific δ2H measurements. For Vicia faba, additionally the δ2H values of n-C31 could be evaluated robustly. With regard to hemicellulose-derived monosaccharides, arabinose and xylose were most abundant and their δ18O values were therefore used to calculate weighted mean leaf δ18Osugar values. Both δ2Hn-alkane and δ18Osugar yielded significant correlations with δ2Hleaf-water and δ18Oleaf-water, respectively (r2 = 0.45 and 0.85, respectively; p < 0.001, n = 24). Mean fractionation factors between biomarkers and leaf water were found to be −156 ‰ (ranging from −133 to −192 ‰) for εn-alkane/leaf-water and +27.3 ‰ (ranging from +23.0 to 32.3 ‰) for εsugar/leaf-water, respectively. Using rearranged Craig-Gordon equations with either Tair or Tleaf and measured δ2Hleaf-water or δ18Oleaf-water as input variables, we furthermore modeled climate chamber RHair and RHleaf values. Modelled RHair values, from the more simplified Craig-Gordon model, turned out to be most accurate and correlate highly significantly with measured RHair values (R2 = 0.84, p < 0.001; RMSE = 6 %). When combining δ2Hleaf-water and δ18Oleaf-water values that are calculated from the alkane and sugar biomarkers instead of actually measured δ2Hleaf-water and δ18Oleaf-water as input variables, the correlation of modelled RHair values with measured RHair values is getting worse, but is still highly significant with R2 = 0.54, p < 0.001; RMSE = 10 %. This highlights the potential of the coupled δ2Hn-alkane-δ18Osugar paleohygrometer approach for suitable relative humidity reconstructions. Finally, the reconstructed source water isotope composition (δ2Hs and δ18Os) as calculated from the coupled approach matches the source water in the climate chamber experiment (δ2Htank-water and δ18Otank-water).

Hill, P.S., Schauble, E.A., Tripati, A., 2020. Theoretical constraints on the effects of added cations on clumped, oxygen, and carbon isotope signatures of dissolved inorganic carbon species and minerals. Geochimica et Cosmochimica Acta 269, 496-539.


Carbonate clumped isotope thermometry has emerged as a useful tool for the reconstruction of precipitation temperatures for minerals from surface and subsurface environments. Few studies have examined the impact of variable solution chemistry and mineral chemistry on clumping. Therefore, we used theoretical calculations to predict the impact of the presence of cations in a solution on the equilibrium clumped, oxygen (18O/16O and 17O/16O, θ and κ), and carbon isotopic (13C/12C) compositions of dissolved inorganic carbon species (DIC), and the impact of cation type and stoichiometry on carbonate mineral composition within the calcite-dolomite-magnesite solid solution. We examined the impact of the presence of Mg2+, K+, Na+, and Ca2+ on equilibrium Δ63

values of carbonate ion groups in DIC species and the composite DIC pool using the B3LYP/6-311++G(2d, 2p) model. We developed new cluster models for dolomite, magnesite, and high-magnesium calcite

(Ca0.83Mg0.17)CO3 and (Ca0.67Mg0.33)CO3) and examined the effect of extraneous cations substituted into the crystal lattices of the carbonate minerals. We find the presence of added cations in the DIC pool increases equilibrium Δ63 values slightly, depending upon their solution concentrations. For the cations examined, the identity of the added cation does not seem to be significant. Cumulative effects may account for small-scale differences (<0.02‰) but are unlikely to be substantial unless cation/anion association and ion pairing are important in the solution that carbonates are growing from. We also find that at a given temperature, stoichiometric dolomite and magnesite Δ63 values are similar to calcite and less than aragonite. Surprisingly, substitution of an extraneous cation into a carbonate mineral (e.g., as observed in high-magnesium calcite) generally lowered Δ63 by a slight amount, which suggests that high and low-magnesian calcites may have resolvable differences in equilibrium clumped isotope signatures, potentially providing an explanation for observations of different Δ47 values in slow-growing minerals. These results imply the cationic composition of the solution may be a minor factor that should be considered for crystals that rapidly grow from solution, and that cationic substitution into carbonate mineral lattices will influence equilibrium compositions of carbonate minerals. Solution chemistry effects on mineral composition are likely to be observed at high growth rates. In contrast, equilibrium isotope compositions arising from cationic substitution in minerals, such as differences between high-Mg calcite and low-Mg calcite, or high-Mg calcite and dolomite, would likely be observed at slow growth rates.

Hirano, K., Hara, T., Ardianor, Nugroho, R.A., Segah, H., Takayama, N., Sulmin, G., Komai, Y., Okada, S., Kawamura, K., 2019. Detection of the oil-producing microalga Botryococcus braunii in natural freshwater environments by targeting the hydrocarbon biosynthesis gene SSL-3. Scientific Reports 9, 16974.

https://doi.org/10.1038/s41598-019-53619-y

The green microalga Botryococcus braunii produces hydrocarbon oils at 25–75% of its dry weight and is a promising source of biofuel feedstock. Few studies have examined this species’ ecology in natural habitats, and few wild genetic resources have been collected due to difficulties caused by its low abundance in nature. This study aimed to develop a real-time PCR assay for specific detection and quantification of this alga in natural environments and to quantify spatiotemporal variations of wild B. braunii populations in a tropical pond. We designed PCR primers toward the hydrocarbon biosynthesis gene SSL-3 and examined amplification specificity and PCR efficiency with 70 wild strains newly isolated from various environments. The results demonstrated that this PCR assay specifically amplified B. braunii DNA, especially that of B-race strains, and can be widely used to detect wild B. braunii strains in temperate and tropical habitats. Field-testing in a tropical pond suggested a diurnal change in the abundance of B. braunii in surface water and found B. braunii not only in surface water, but also at 1–1.5 m deep and in bottom sediments. This method can contribute to efficient genetic resource exploitations and may also help elucidate the unknown ecology of B. braunii.

Hirose, T., Tanikawa, W., Hamada, Y., Lin, W., Hatakeda, K., Tadai, O., Wu, H.Y., Nomura, S., Abe, N., Gupta, L.P., Sugihara, T., Masaki, Y., Kinoshita, M., Yamada, Y., 2019. Strength characteristics of sediments from a gas hydrate deposit in the Krishna–Godavari Basin on the eastern margin of India. Marine and Petroleum Geology 108, 348-355.


Knowledge of the strength of sediments overlying sub-seafloor gas-hydrate deposits is crucial for predicting borehole and seafloor stability during hydrate extraction. Ideally, sediment strength should be determined along a continuous downhole profile from the seafloor to the hydrate reservoir, but few such profiles have been obtained. In this study we used cores retrieved at Site NGHP-02-23 in the Krishna–Godavari Basin in unconfined penetration tests on split cores and in triaxial deformation experiments on hydrate-free sediment samples. Although penetrometer tests identified relatively low strength (70–250 kPa) likely due to hydrate dissociation in the hydrate-bearing interval 90–300 m below seafloor (mbsf), sediment strength exceeded 350 kPa in the intervals 140–170 and 250–270 mbsf, each of which lies just above a zone of high gas-hydrate concentration. The average stress ratio of triaxial strength at 4% axial strain to effective mean stress (qε=4%/p’) of hydrate-free silts was about 0.67 throughout the Hole. An exception to this trend was in fine sands from 280

mbsf in the deeper gas-hydrate zone, where the stress ratios were greater than 1.0. The stress ratios of hydrate-bearing sediments in the deeper gas-hydrate zone that were reported from the pressure-core measurements were far greater than those of any hydrate-free sediments for a given effective mean stress. The high-strength intervals in silty sediments we identified by the penetration tests could be associated with zones of high hydrate concentration. Because high-strength layers in fine-grained silty sediments commonly exhibit lower permeability than sandy layers (potential hydrate-host), they may act as seals that assist the precipitation of hydrate below them.

Hirslund, F., Morkel, P., 2020. Managing the dangers in Lake Kivu – How and why. Journal of African Earth Sciences 161, 103672.


Lake Kivu is probably the World's largest natural freshwater digester of algae to produce biogas. Its resources in situ may generate power for generations. Extracting gas is essential to avert a future limnic eruption. Undisturbed, the reservoir formed by salinity-based chemoclines, keeps biogenic CH4 and CO₂ in solution. This is stored in lower strata of the lake.

Gases accumulating ever closer to saturation levels, threaten to cause a future limnic eruption. An eruption as occurred at Lake Nyos in Cameroon in 1986 with 1746 casualties, can result if not prevented. But Lake Kivu has potential and inventory for consequences 1000 times larger.

Based on novel hypotheses on vertical transport and the lake's history, we used multidisciplinary analyses of this situation. One can foresee its outcomes and recognise system constraints.

Therefore, initiating gas extraction enables the vital outcomes; (a) society can enforce extraction methods that ensure prevention of future disasters while, (b) minimizing environmental impact, (c) maximizing useful energy output, and (d) developers pursuing economic projects. The key to safety is management of the chemoclines while producing gas. Achieving safety and production needs the right specification of plant design. For gas production facilities, it is designing to achieve what must be done technically.

After our primary concern for public safety, we examine ways of minimizing any environmental impacts. Changes are caused by natural upwelling of saline meteoric water from lava strata into the deep monimolimnion of nutrient-rich water bodies. Raw gas extracted must be washed with water from the mixolimnion to make the gas fit for use in power-generation and domestic gas.

For maintenance of chemoclines, we discuss how a fraction of the degassed water must be evacuated from the resource strata and re-injected into the mixolimnion to maintain chemoclines. The challenge lies in how to minimize this safety-driven impact on the mixolimnion from toxic effects of H₂S, from CO₂-induced acidity, and oxygen depletion by CH4 and H₂S.



India's National Gas Hydrate Program Expedition 2 (NGHP-02) completed an ambitious pressure coring program as part of their effort to evaluate gas hydrate in coarse-grained reservoirs in the Bay of Bengal. The 75 successful pressure cores were used to measure gas hydrate saturation, examine the morphology of the gas hydrate at in situ conditions, and to provide samples for further laboratory work. Pressure core quality was assessed via pressure-temperature records and X-ray computed tomographic reconstructions of cores. Gas hydrate saturations were measured by using the gas from quantitative degassing experiments in methane mass balance calculations. Gas hydrate morphology was determined from X-ray computed tomographic reconstructions, P-wave velocity, and gamma density measured under pressure using PCATS, the Pressure Core

Analysis and Transfer System. Gas hydrate saturations reached 65–85% in the pores of sandy reservoir sediments, and were near full saturation in gravelly sediments. Clayey interlayers between reservoir sediments had gas hydrate saturations near 10%, with no evidence of gas hydrate veins in X-ray computed tomographic (CT) reconstructions. Veins of gas hydrate were visible in X-ray images of clayey non-reservoir sediments; at some locations the full complement of gas hydrate was contained in X-ray-resolveable veins, but in others the veins only accounted for part of the total gas hydrate burden in the sediment, implying that some gas hydrate was finely distributed in the pore space or in veins below the resolution of the X-ray CT data. At one location low-density, biosilica-rich silty clays hosted pore-filling gas hydrate at saturations of 45%, with only slightly elevated P-wave velocities. Gas hydrate saturation and morphology from all the pressure cores are presented here and placed into geological context.

Horgby, Å., Segatto, P.L., Bertuzzo, E., Lauerwald, R., Lehner, B., Ulseth, A.J., Vennemann, T.W., Battin, T.J., 2019. Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains. Nature Communications 10, 4888.

https://doi.org/10.1038/s41467-019-12905-z

Inland waters, including streams and rivers, are active components of the global carbon cycle. Despite the large areal extent of the world’s mountains, the role of mountain streams for global carbon fluxes remains elusive. Using recent insights from gas exchange in turbulent streams, we found that areal CO2 evasion fluxes from mountain streams equal or exceed those reported from tropical and boreal streams, typically regarded as hotspots of aquatic carbon fluxes. At the regional scale of the Swiss Alps, we present evidence that emitted CO2

derives from lithogenic and biogenic sources within the catchment and delivered by the groundwater to the streams. At a global scale, we estimate the CO2 evasion from mountain streams to 167 ± 1.5 Tg C yr−1, which is high given their relatively low areal contribution to the global stream and river networks. Our findings shed new light on mountain streams for global carbon fluxes.

Hsiung, K.-H., Saito, S., Kanamatsu, T., Sanada, Y., Yamada, Y., 2019. Regional stratigraphic framework and gas hydrate occurrence offshore eastern India: Core-log-seismic integration of National Gas Hydrate Program Expedition 02 (NGHP-02) Area-B drill sites. Marine and Petroleum Geology 108, 206-215.


The Indian National Gas Hydrate Program Expedition 02 (NGHP-02) was designed to study the occurrence of gas hydrate along the passive continental margin of the Indian Peninsula in the Bay of Bengal. Twelve holes were logged and measured with logging-while-drilling (LWD) and five holes were cored in Area-B of NGHP-02. The LWD and coring results in Area-B helped to understand the geological significance of sequence stratigraphy in Krishna-Godavari Basin and identified the occurrence of gas hydrate. This study summarized the log- and litho-units in Area-B and establish three integrated units based on the core-log-seismic integration. Most of the downhole log and core inferred gas hydrate occurrences are in the Late Miocene Integrated-Unit B with several sets of reservoir sections exhibiting favorable conditions for hosting gas hydrate. The gas hydrates reservoirs associated with reflectors R1 and R2 were identified and the R1 reservoirs are characterized by fracture- and pore-filling gas hydrate, and the R2 is in sand-rich sediments with pore-filling gas hydrate at high saturations. The thickness variations associated with the R1 and R2 are possibly associated with the development anticlinal structure and are likely related to syn-sedimentary growth of the folding structures. Major gas hydrate zones exist in and around the R1 and R2 near the BSR depth, and mostly have coincident with the fractures and mass-transport deposits. The spatial distribution of gas hydrate in the R1 and R2 reservoirs is highly influenced by the anticlinal structure. This study can be considered a good case for the future gas hydrate studies and explorations in the nearby areas.

Hsu, C.-W., MacDonald, I.R., Römer, M., Pape, T., Sahling, H., Wintersteller, P., Bohrmann, G., 2019. Characteristics and hydrocarbon seepage at the Challenger Knoll in the Sigsbee Basin, Gulf of Mexico. Geo-Marine Letters 39, 391-399.

https://doi.org/10.1007/s00367-019-00595-x

Active seafloor hydrocarbon seepage from three distinct, positive seafloor features, termed knolls, in the Sigsbee Knolls area, Gulf of Mexico (GOM), was investigated in March 2015. The study sites included the Challenger Knoll, which was drilled by the Deep Sea Drilling Program (DSDP) in 1969 and showed the influence of salt tectonics on its evolution and the presence of subsurface petroleum. This study used gas flare mapping in the water column, detailed seafloor bathymetry, backscatter mapping, sub-bottom profiling, and remote sensing of surface water to locate seafloor areas of hydrocarbon emissions. Flares of gas bubbles were detected in the water column above all three knolls, making them the deepest reported gas emission sites in the GOM. Although surface oil slicks above the Sigsbee Knolls have been detected by satellite imaging in the past; in this study, neither satellite imagery nor ship-based observations detected floating oil, this suggests that oil seepage in the region is intermittent. High-resolution video surveys of the seafloor at Challenger Knoll, using a camera system mounted on a lowered tow-vehicle, documented the presence of seep-related chemosynthetic fauna including clam fields and microbial mats at the western part of the knoll. These findings are consistent with previous investigations that link hydrocarbon seepage at Challenger Knoll to salt tectonics. During visual seafloor inspections, no asphalt deposits, such as those known from sites in the Campeche Knoll area in the southern GOM, were observed. These findings indicate that hydrocarbon seepage is less pronounced in the Sigsbee Knolls region, central GOM, than is the case in hydrocarbon systems in the northern or southern GOM.

Hu, C., Wang, C., He, L., Han, X., 2019. Novel strategies for enhancing shotgun lipidomics for comprehensive analysis of cellular lipidomes. TrAC Trends in Analytical Chemistry 120, 115330.


Shotgun lipidomics is one of the most powerful tools in analysis of cellular lipidomes in lipidomics, which directly analyzes lipids from lipid extracts of diverse biological samples with high accuracy/precision. However, despite its great advances in high throughput analysis of cellular lipidomes, low coverage of poorly ionized lipids, especially those species in very low abundance, and some types of isomers within complex lipid extracts by shotgun lipidomics remains a huge challenge. In the past few years, many strategies have been developed to enhance shotgun lipidomics for comprehensive analysis of lipid species. Chemical derivatization represents one of the most attractive and effective strategies, already receiving considerable attention. This review focuses on novel advanced derivatization strategies for enhancing shotgun lipidomics. It is anticipated that with the development of enhanced strategies, shotgun lipidomics can make greater contributions to biological and biomedical research.

Hu, Y.-Z., Young, G.C., Burrow, C., Zhu, Y.-a., Lu, J., 2019. High resolution XCT scanning reveals complex morphology of gnathal elements in an Early Devonian arthrodire. Palaeoworld 28, 525-534.


Arthodire placoderms, as a possible sister group of Chinese ‘maxillate’ placoderms plus crown gnathostomes, provide important information regarding early evolution of jaws and teeth. High-resolution computed tomography and digital dissection on a unique articulated 400 million-year-old buchanosteid arthrodire permitsa detailed description of the three types of gnathal elements in basal arthrodires for the first time, giving insights into their morphology and the organization of the associated dentition. In displaying numerous denticle rows (dental fields), the gnathal element morphology is very different from the much-reduced denticulation of higher brachythoracid arthrodires, even though the latter have been used recently to interpret origin and early evolution of teeth. Ossification centres are anterolateral on the anterior supragnathal (attached to the braincase), anteromesial on the posterior supragnathal (attached to the palatoquadrate), and in the central part of the biting portion of the infragnathal (attached to the meckelian cartilage). The latter bone shows no evidence of two ossification centres as has been interpreted for more advanced arthrodires. Denticle rows radiating from the ossification centre form dental fields in all three elements, and are more similar to the gnathal elements of phlyctaeniid and actinolepid arthrodires than to advanced brachythoracids. The new evidence gives insights into the primitive arthrodire condition for comparison with the dermal jaw bones of Chinese ‘maxillate’ placoderms that have been homologised with the premaxilla, maxilla, and dentary of osteichthyans. The new details will

help clarify the sequence of character acquisition in the evolution of marginal jaw bones in basal gnathostome groups.

Hu, Y.-Z., Young, G.C., Lu, J., 2019. The Upper Devonian tetrapodomorph Gogonasus andrewsae from Western Australia: Reconstruction of the shoulder girdle and opercular series using X-ray Micro-Computed Tomography. Palaeoworld 28, 535-542.


The tetrapodomorph fish, Gogonasus andrewsae is a three dimensionally well-preserved sarcopterygian from the Gogo Formation (Frasnian, early Upper Devonian, ∼380 million years ago) in Western Australia. High-resolution X-ray Micro-Computed Tomography and 3D printouts were used to obtain a digital reconstruction of its shoulder girdle and opercular series. Our new findings show the opercular series in a close fit against the upper bones of the shoulder girdle only if the anocleithrum, supracleithrum and post-temporal are aligned more horizontally than in previous reconstructions. The lowermost subopercular bone also differs, in partly covering the clavicle of the shoulder girdle. The ascending process of the clavicle, and the ventral process of the anocleithrum, do not fit closely inside the cleithrum, and perhaps functioned for ligamentous attachment. A rugose area on the anocleithral process is in a similar relative position to the attachment of a muscle ligament on the shoulder girdle of various living actinopterygians. Our manipulation of 3D printouts permits testing of the morphological fit of extremely fragile acid-etched bones, and indicates a new way to investigate the constructional morphology of one or more mechanical units of the vertebrate skeleton. It is suggested that Micro-CT imaging, reconstruction, visualisation and 3D printing techniques will provide a rigorous new test leading to modification of previous reconstructions of extinct vertebrates that were based on graphical methods and 2D imaging.

Hu, Y., Cai, B., Huan, T., 2019. Enhancing metabolome coverage in data-dependent LC–MS/MS analysis through an integrated feature extraction strategy. Analytical Chemistry 91, 14433-14441.


In untargeted metabolomics, conventional data preprocessing software (e.g., XCMS, MZmine 2, MS-DIAL) are used extensively due to their high efficiency in metabolic feature extraction. However, these programs present limitations in recognizing low-abundance metabolic features, thus hindering complete metabolome coverage from the analysis. In this work, we explored the possibility of enhancing the metabolome coverage of data-dependent liquid chromatography–tandem mass spectrometry (LC–MS/MS) results by rescuing metabolic features that are missed by conventional software. To achieve this goal, we first categorized the metabolic features into four confidence levels based on their chromatographic peak shapes and the presence of corresponding MS/MS spectra. We then assessed the false positives and quantitative accuracy of the metabolic features that contain MS/MS spectra but are not recognized by conventional software. Our results indicate that these missed features contain valid and important metabolic information and should be integrated into the conventional metabolomics results. Thus, we developed a data-preprocessing pipeline to extract low-abundance metabolic features and integrate them with the results from conventional programs. This integrated feature extraction strategy was tested on a set of fecal metabolomic data retrieved from mice who have undergone normal diet vs high-fat diet treatments. In our test data set, the integrated feature extraction approach increased the number of significant features being extracted by 24.4% and identified five additional metabolites bearing critical biological meanings. Our results show that this integrated feature extraction strategy remarkably improves the metabolome coverage beyond that of conventional data preprocessing, therefore facilitating the confirmation of metabolites of interest and accomplishment of a higher success rate in de novo metabolite identification.

Huang, C., Liu, G., Ma, Y., Zhou, X., Zhang, L., Yin, J., Guo, J., 2019. Hydrocarbon migration in fracture-cave systems of carbonate reservoirs under tectonic stresses: A modeling study. Petroleum Research 4, 354-364.


The Tahe oilfield, located in the southwest of the Akekule nosing structure, northern Tarim basin, was the most prolific oilfield targeting at the Ordovician carbonate reservoirs in China. The reservoir space was dominant with fracture-cave systems commonly induced by tectonics and karstification. Although hydrocarbon production had proceeded for two decades in the Tahe oilfiled, the control of oil and gas accumulations was still doubtful. In this work, the periodic fluid flow induced by cyclic tectonic stresses was proposed as the mechanism of hydrocarbon migration in the fracture-cave systems of carbonate reservoirs. The fracture networks formed conduits for fluid flow, and the fluid pressure in caves transmitted from stress field provided the driving force. The constitutive equations were established among stresses, fracture densities and flow velocities. Four quasi-3D geological models were constructed to simulate the flow velocities on the Ordovician surface of Akekule nosing structure in the critical tectonic stages. The simulated results supplied indicative information on oil and gas migration and accumulation in the tectonic stages. Combining with the oil and gas charge history, a conceptual model was built to reveal the multi-stage oil and gas charge and accumulation in the Ordovician of Akekule nosing structure.

Huang, H., Li, R., Jiang, Z., Li, J., Chen, L., 2020. Investigation of variation in shale gas adsorption capacity with burial depth: Insights from the adsorption potential theory. Journal of Natural Gas Science and Engineering 73, 103043.


In this study, the Polanyi theory was applied to investigate variation in shale gas adsorption capacity with burial depth. Analyses were implemented on background data of two shale samples with respective TOC contents of 4.00% and 4.51% TOC, accompanied by combination of the Polanyi theory and isothermal adsorption parameters. Shale gas adsorption capacity was found to first increase and then decrease as the burial depth grew, and the burial depth corresponding to the maximum adsorption capacity was basically constant within the study area. Specifically, pressure coefficient had the largest impact on the minimum adsorption potential, reaching 1.721 mol/kJ, while the ground temperature gradient was the most influential factor on the burial depth corresponding to the maximum adsorption capacity, reaching 1080 m. When the burial depth was shallower than 3200 m, the pressure coefficient dominated, whereas in deeper parts, the ground temperature gradient became dominant.


https://doi.org/10.1007/s10532-019-09888-5

Tetrahydrofuran (THF) is a ubiquitous toxic and carcinogenic pollutant. Screening for pure or mixed-culture microorganisms that can efficiently degrade THF is difficult due to its chemical stability. In this study, an enrichment culture, H-1, with a stable THF-degrading ability and microbial community structure was enriched from activated sludge and could efficiently degrade 95% of 40 mM THF within 6 days. The optimal THF degradation conditions for H-1 were an initial pH of 7.0–8.0 and a temperature of 30 °C. The substrate tolerance concentration of H-1 reached 200 mM. Heavy metals tolerance concentrations of Cu2+, Cd2+ and Pb2+ of H-1 was 0.5 mM, 0.4 mM and 0.03 mM, and 4 mM Mn2+ did not significantly influence the THF degradation ratio or biomass of H-1. H-1 might be a good material for actual wastewater treatment because of its efficient THF degradation performance and ability to resist various stressful conditions. In addition, the THF-degrading efficiency of H-1 was enhanced by the addition of moderate carbon sources. High-throughput sequencing of the 16S rRNA gene showed that Rhodococcus sp. (a potential THF-degrading strain) and Hydrogenophaga sp. (a potential non-THF-degrading strain) were the dominant microorganisms in the H-1 culture. These results indicate the potential coexistence of cooperation and competition between THF-degrading bacteria and nondegrading bacteria in this enrichment culture.

Huang, J.-Y., Martínez-Pérez, C., Hu, S.-X., Donoghue, P.C.J., Zhang, Q.-Y., Zhou, C.-Y., Wen, W., Benton, M.J., Luo, M., Yao, H.-Z., Zhang, K.-X., 2019. Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography. Palaeoworld 28, 429-440.


The composition of conodont apparatuses is crucial for understanding the feeding mechanisms of these early vertebrates. However, the multielement apparatus reconstructions of most species remain equivocal because they have been inferred from loose element collections, guided by knowledge from rare articulated ‘bedding plane assemblages’ and fused clusters, often from distantly related taxa. Even these natural assemblages can be difficult to interpret because the component elements can be closely juxtaposed or embedded in matrix, making it hard to discern the morphology of each element and their relative positions within the architecture of the feeding apparatus. Here we report five exceptionally preserved conodont clusters from the Middle Triassic Luoping Biota, Yunnan Province, Southwest China. These materials were scanned using synchrotron radiation X-ray tomographic microscopy (SRXTM), revealing the morphology and positional homology of the component elements in the fused clusters. We confirm that the apparatus of Nicoraella was composed of eight types of elements, comprising a total of 15 elements. SRXTM reveals the positional homologies of the component elements, viz. a single alate element is located in the S0 position, flanked successively abaxially by pairs of breviform digyrate S1 and S2 elements, bipennate S3 and S4 elements, and a pair of inwardly curved breviform digyrate M elements. Carminate elements occupy the P1 and P2 positions. The apparatus of Nicoraella is among the most completely characterised of all conodonts and serves as a template for the reconstruction of gondollellids.

Hughes, S.A., Naile, J., Pinza, M., Ray, C., Hester, B., Baum, J., Gardiner, W., Kallestad, W., Brzuzy, L., 2019. Characterization of miscellaneous effluent discharges from a mobile offshore drilling unit to the marine environment. Environmental Toxicology and Chemistry 38, 2811-2823.


A study was performed to evaluate the potential biological impacts from 8 different miscellaneous discharges from an oil and gas mobile offshore drilling unit (MODU) including deck drainage, desalination unit waste, boiler blowdown, fire control system test water, noncontact cooling water, and bilge water. Samples were evaluated for toxicity using a rapid (<1 h) initial screening test (echinoderm [Dendraster excentricus] fertilization test), and if toxicity was found, further testing was conducted using 3 chronic whole‐effluent toxicity tests. This additional testing included the embryo larval development 72‐h echinoderm (D. excentricus); 7‐d mysid (Americamysis bahia) survival, growth, and fecundity invertebrate test; and 7‐d topsmelt (Atherinops affinis) survival and growth fish test. Toxicity identification evaluations were performed on 3 discharges that consistently elicited a toxic response during whole‐effluent toxicity testing. To place the results of the toxicity testing into the context of environmental risk, the spatial extent of potential biological effects was investigated using the CORMIX mixing zone model. The output of the modeling indicated that discharge of selected effluents did not result in concentrations, or duration of exposure, that would elicit toxic effects to organisms living in the surrounding environment. The present study provides a comprehensive data set that was used to characterize potential toxicity and environmental risk of MODU “miscellaneous discharges” which could help inform future risk assessments of these discharges.

Humez, P., Osselin, F., Wilson, L.J., Nightingale, M., Kloppmann, W., Mayer, B., 2019. A probabilistic approach for predicting methane occurrence in groundwater. Environmental Science & Technology 53, 12914-12922.


Aqueous geochemistry datasets from regional groundwater monitoring programs can be a major asset for environmental baseline assessment (EBA) in regions with development of natural gases from unconventional hydrocarbon resources. However, they usually do not include crucial parameters for EBA in areas of shale gas development such as methane concentrations. A logistic regression (LR) model was developed to predict the probability of methane occurrence in aquifers in Alberta (Canada). The model was calibrated and tested using geochemistry data including methane concentrations from two groundwater monitoring programs. The LR model correctly predicts methane occurrence in 89.8% (n = 234 samples) and 88.1% (n = 532 samples) of groundwater samples from each monitoring program. Methane concentrations strongly depend on the occurrence of electron donors such as sulfate and to a lesser extent on well depth and the total dissolved solids

of groundwater. The model was then applied to a province-wide public health groundwater monitoring program (n = 52,849 samples) providing aqueous geochemistry data but no methane concentrations. This approach allowed the prediction of methane occurrence in regions where no groundwater gas data are available, thereby increasing the resolution of EBA in areas of shale gas development by using basic hydrochemical parameters measured in high-density groundwater monitoring programs.


https://doi.org/10.1029/2019GL083401

CO2 geosequestration in oil reservoirs is an economically attractive solution as it can be combined with enhanced oil recovery (CO2‐EOR). However, the effectiveness of the associated three‐phase displacement processes has not been tested at the micrometer pore scale, which determines the overall reservoir‐scale fluid dynamics and thus CO2‐EOR project success. We thus imaged such displacement processes in situ in 3‐D with X‐ray microcomputed tomography at high resolution at reservoir conditions and found that oil extraction was enhanced substantially, while a significant residual CO2 saturation (13.5%) could be achieved in oil‐wet rock. Statistics of the residual CO2 and oil clusters are also provided; they are similar to what is found in analogue two‐phase systems although some details are different, and displacement processes are significantly more complex.

Ijiri, A., Haraguchi, S., Jiménez-Espejo, F.J., Komai, N., Suga, H., Kinoshita, M., Inagaki, F., Yamada, Y., 2019. Origin of low-chloride fluid in sediments from the eastern continental margin of India, results from the National Gas Hydrate Program Expedition 02. Marine and Petroleum Geology 108, 377-388.


National Gas Hydrate Program Expedition 02 was conducted in 2015 by D/V Chikyu in the western Bay of Bengal, India. Analyses of interstitial water in sediment from four drilling sites along the eastern and western transect in the Krishna–Godavari Basin show that dissolved chloride (Cl−) concentrations decreased with depth from seawater values (>550 mM) near the sediment surface to 300–400 mM at 350–400 m below seafloor (mbsf), suggesting the upward advection of low-Cl– fluid. Excursions of Cl− concentrations toward low values in gas hydrate zones were attributed to the presence of fresh water released by dissociation of gas hydrate during core recovery. At Sites in the western transect, Cl− concentrations below the gas hydrate reservoir (around 280 mbsf) were ca. 60 mM and ca. 45 mM lower than those from above the reservoir, and δ18O and δD values were 1–2‰ and 0.7–1.3‰ higher than those from above the reservoir, respectively. These results suggest that a fraction of migrating low-Cl– fluid is trapped in the gas hydrate zone, causing decreases of δ18O and δD in the residual water due to isotopic fractionation during gas hydrate formation. From mass-balance calculations, we estimated that 10–20% of the advected fluid is trapped at the gas hydrate zone. At all sites, the δ18O and δD values below the gas hydrate zone, representing relatively unaltered low-Cl– fluid, were 0.5–1‰ higher and ca. 13–15‰ lower than those of seawater, respectively. This trend is consistent with water derived from the dehydration of clay minerals, which generally occurs in deeply buried sediments. The contribution of clay mineral dehydration is relatively large at the western transect compared to that in the eastern transect. Our results imply that fluid advection contributes to the accumulation of gas hydrate in the study area.

Inan, M.A., Kavak, O., 2019. Shale resource potential of the Silurian Dadas Formation in Diyarbakır (SE Anatolia of Turkey) and its surroundings. Arabian Journal of Geosciences 12, 679.

https://doi.org/10.1007/s12517-019-4837-7

More than 70% of the estimated producible unconventional oil and gas reserves of Turkey are reported to be in the Dadas Formation located in Southeastern Anatolia. In this study, shale resource potential of the Dadas Formation was examined with samples taken from the A2 well which were analyzed in terms of mineralogy,

organic geochemistry. These data were placed into context using a composite log obtained from the wells that penetrated the Dadas Formation. TOC contents of the formation range from 1.1 to 4.92 wt%, and Tmax values range from 431 to 451 °C. XRD mineral analysis has shown that the samples contain 73.07% illite, 3.28% smectite, 19.53% kaolinite, and 4.14% chlorite on average. The kerogen type of samples are in the fair oil origin zone. Although the Dadas Formation has low values of silica content and brittleness, these values make it valuable for consideration of the Dadas Formationability to produce shale gas. According to analysis, the Dadas shale may have limited shale oil potential.

Iqubal, M.A., Sharma, R., Kamaluddin, Jheeta, S., 2019. Synthesis of nucleic acid bases by metal ferrite nanoparticles from a single carbon atom precursor molecule: Formamide. Origins of Life and Evolution of Biospheres 49, 147-162.

https://doi.org/10.1007/s11084-019-09585-6

The synthesis of prebiotic molecules from simple precursors is believed to be a crucial scheme in order to study the origin of life processes. The present study describes the one-pot synthesis of purine and pyrimidine nucleic acid bases in the presence of pre-biologically significant binary metal oxide nanoparticles, metal ferrites, namely NiFe2O4, CoFe2O4, CuFe2O4, ZnFe2O4 and MnFe2O4. The products identified are cytosine, isocytosine, 4(3H)-pyrimidinone, adenine, hypoxanthine and purine. The ability of isocytosine (a constitutional isomer of cytosine) to recognize cytosine and guanine through normal and reversed Watson-Crick pairing respectively, demonstrates an important storyline for the genesis of ancient nucleic acids. The relevance of other synthesized nucleic acid bases with respect to the origin of life is also discussed. The divalent metal ions in iron oxide make it an appropriate catalytic system because it demonstrates excellent catalytic performance for the nucleic acid bases synthesis with significantly high yield, as compared to pure iron oxide and some other minerals like silica, alumina, manganese oxides and double metal cyanide complexes.

Ishibashi, Y., Aoki, K., Okino, N., Hayashi, M., Ito, M., 2019. A thraustochytrid-specific lipase/phospholipase with unique positional specificity contributes to microbial competition and fatty acid acquisition from the environment. Scientific Reports 9, 16357.

https://doi.org/10.1038/s41598-019-52854-7

Thraustochytrids are heterotrophic marine protists that are considered as important decomposers in the marine ecosystem; however, how they digest and uptake lipid nutrients from the environment is largely unknown. Genomic clustering analysis using thraustochytrid draft genome databases revealed that novel proteins with a Lipase_3 domain are commonly present in thraustochytrids, including Aurantiochytrium limacinum. After heterologous expression and His tag-based purification, protein ID: 145138 was identified as lipase/phospholipase capable of hydrolyzing triacylglycerol (TG) and phosphatidylcholine (PC). 145138 was secreted into the medium, and deletion of the 145138 gene in A. limacinum reduced the degradation of extracellular lipids. Fatty acids generated by 145138 were reused for the biosynthesis of PC and TG, and 145138 allowed A. limacinum to survive in the medium containing TG as a sole carbon source. 145138 hydrolyzed all the acyl-ester linkages of TG; however, the enzyme showed strict positional specificity toward phospholipids, generating 2-acyl lysophospholipids. The 2-acyl lysophospholipids showed stronger antimicrobial activity compared with 1-acyl lysophospholipids. These results suggested that 145138 is a bifunctional enzyme that contributes to the acquisition of lipid nutrients from the environment, as well as to generate antimicrobial lysophospholipids that are beneficial for competition with bacteria over lipid nutrients in the marine environment.

Iwase, M., Liang, Y., Masuda, Y., Morimoto, M., Matsuoka, T., Boek, E.S., Kaito, Y., Nakagawa, K., 2019. Application of a digital oil model to solvent-based enhanced oil recovery of heavy crude oil. Energy & Fuels 33, 10868-10877.


To investigate enhanced oil recovery processes, we constructed a molecular model of a live heavy crude oil (digital oil) and studied the crude oil properties at the reservoir temperature and a wide range of pressures. We identified the liquid phase components of the digital oil by flash calculation and calculated the density and viscosity by molecular dynamics simulations. The calculated density and viscosity were in good agreement with experimental data. To evaluate the effectiveness of various solvents to enhance oil recovery, we calculated the oil property changes when different solvents were added to the digital oil. First, we compared methane and carbon dioxide (CO2). The results indicated that CO2 was more effective in terms of oil-viscosity reduction, oil swelling, and diffusion in the oil. Second, we evaluated the effectiveness of 11 different solvents: nitrogen, CO2, methane, ethane, propane, n-heptane, n-octane, toluene, and three xylene isomers (o-xylene, m-xylene, and p-xylene). Ethane had the greatest effect on oil-viscosity reduction and oil swelling, and CO2 had the highest diffusion coefficient. From these results, ethane and CO2 are appropriate solvents for this crude oil. In addition, it is interesting to note that the decreases of the viscosity among the three xylene isomers were different, but there were no differences in the swelling factors and diffusion coefficients. The different rotation motion characteristics of the xylene isomers can account for the viscosity differences. Such information will be helpful for further development of digital oil models.

Jagadisan, A., Heidari, Z., 2019. Experimental quantification of the effect of thermal maturity of kerogen on its wettability. SPE Reservoir Evaluation & Engineering 22, 1323-1333.

https://doi.org/10.2118/195684-PA

Kerogen is often considered to be fully hydrocarbon-wet in reservoir characterization. However, wettability of kerogen is not well-understood and quantified. Thermal maturation induces changes in the chemical structure of kerogen and alters its oxygen (O) and hydrogen (H) content. This process affects the surface properties of kerogen and can influence its wettability. Assumptions made regarding the wettability of kerogen affect the interpretation of borehole geophysical measurements such as electromagnetic measurements. Therefore, it is important to quantify the wettability of kerogen as a function of its thermal maturity. The objectives of this research are to experimentally quantify the wettability of kerogen at different thermal-maturity levels and to quantify the influence of chemical composition of kerogen on its wettability. To achieve these objectives, kerogen was first isolated from organic-rich mudrock samples from two different formations at different thermal-maturity levels. The extracted kerogen samples were then synthetically matured. Variations in the composition and chemical-bonding state of carbon (C) present in kerogen at different levels of natural and synthetic thermal maturity were determined using X-ray photoelectron spectroscopy (XPS). The sessile drop method was used to measure the contact angle to quantify the wettability of kerogen. We then investigated the effects of thermal maturity and chemical composition/bonding of kerogen on its wettability.

Kerogen samples from two organic-rich mudrock formations (Formations A and B) were tested, and it was demonstrated experimentally that the wettability of kerogen varies with thermal maturity. Kerogen from Formation A at low thermal maturity formed a 44° air/ water-contact angle and 110° air/oil-contact angle. However, at higher thermal maturities (heat treated at 650°C), the air/water-contact angle increased to 122°, and the oil droplet completely spreads on the kerogen sample. The results suggest that kerogen is oleophilic and hydrophobic at high thermal maturity and hydrophilic at low thermal maturity. The air/water-contact angles in kerogen samples were also recorded after the removal of bitumen generated during synthetic maturation of kerogen using chloroform. The air/water contact angle was shown to increase from 44 to 90° and from 111 to 125° with an increase in thermal maturity in Formations A and B, respectively, in the absence of bitumen. Thus, kerogen becomes hydrophobic with increasing thermal maturity in both the presence and absence of bitumen. The outcomes of this study can potentially improve the formation evaluation of organic-rich mudrocks, in addition to improving our understanding of fluid-flow mechanisms in unconventional reservoirs.

Jain, V., Saumya, S., Vij, J., Singh, J., Singh, B., Pattnaik, S., Oli, A., Kumar, P., Collett, T.S., 2019. New technique for accurate porosity estimation from logging-while-drilling nuclear magnetic resonance data, NGHP-02 expedition, offshore, India. Marine and Petroleum Geology 108, 570-580.


Drilling and acquiring high-quality downhole log data in the gas hydrate–bearing sedimentary sections, found mostly in deep marine environments and at low temperatures, is often challenging because of the disseminated gas hydrates and mostly unconsolidated nature of the host sediments. Logging while drilling (LWD) technology was used in National Gas Hydrate Program Expedition 02 (NGHP-02) in 25 wellbores to acquire data needed for the comprehensive analysis of gas hydrate occurrences offshore eastern India. The LWD tools deployed included a nuclear magnetic resonance (NMR) tool along with a density measurement tool for porosity computation, a high-resolution resistivity imaging tool for fracture evaluation and depositional system identification, and a borehole acoustic tool for gas hydrate identification and pore-pressure monitoring (by measuring deviation of sonic velocity from normal compaction trend).

The NMR LWD tool measures transversely relaxing signal (echoes) decay, which is calibrated and inverted into transverse relaxation times or a T2 distribution (Figure 2). The T2 distribution is then summed to compute NMR porosity. Due to the solid nature of gas hydrates at in situ conditions, they are invisible to NMR. It is fundamental for gas hydrate identification to look for zones with differences between the NMR porosity and density porosity. This paper describes a new evaluation technique that addresses the porosity “deficit problem” due to the fast T2 relaxation observed in NMR data acquired during NGHP-02. In the new algorithm, the T1-T2 distributions are jointly inverted, compared to conventional NMR processing, which inverts a T2 distribution from the echo signal using a constant T1/T2 ratio. It is observed that with the conventional method which assumes a constant T1/T2 ratio, the NMR porosity in gas hydrate bearing zones is underestimated by about 3–6 porosity units, and the derived gas hydrate saturations are overestimated by ∼8–10%.

Jang, J., Dai, S., Yoneda, J., Waite, W.F., Stern, L.A., Boze, L.-G., Collett, T.S., Kumar, P., 2019. Pressure core analysis of geomechanical and fluid flow properties of seals associated with gas hydrate-bearing reservoirs in the Krishna-Godavari Basin, offshore India. Marine and Petroleum Geology 108, 537-550.


Physical properties of the sediment directly overlying a gas hydrate reservoir provide important controls on the effectiveness of depressurizing that reservoir to extract methane from gas hydrate as an energy resource. The permeability of overlying sediment determines if a gas hydrate reservoir's upper contact will provide an effective seal that enables efficient reservoir depressurization. Compressibility, stiffness and strength indicate how overlying sediment will deform as the in situ stress changes during production, providing engineering data for well designs. Assessing these properties requires minimally-disturbed sediment. India's National Gas Hydrates Program Expedition 2 (NGHP-02) provided an opportunity to study these seal sediment properties, reducing disturbance from gas exsolution and bubble growth by collecting a pressure core from the seal sediment just above the primary gas hydrate reservoir at Site NGHP-02-08 in Area C of the Krishna-Godavari Basin. The effective stress chamber (ESC) and the direct shear chamber (DSC) devices in the suite of Pressure Core Characterization Tools (PCCTs) were used to measure permeability, compressibility, stiffness and shear strength at the in situ vertical stress. Geotechnical properties of the predominantly fine-grained seal layer at in situ vertical stress are in typical clay sediment ranges, with low measured permeability (0.02 mD), high compressibility (Cc = 0.26–0.33) and low shear strength (404 kPa). Though pressure and temperature were maintained throughout the collection and measurement process to stabilize gas hydrate, the lack of effective stress in the pressure core storage chamber and the chamber pressurization with methane-free water caused core expansion and gas hydrate in a thin coarser-grained layer to dissolve. The PCCTs can reapply in situ stress with incremental loading steps during a consolidation test to account for sediment compaction. Gas hydrate dissolution can be limited by storing cores just above freezing temperatures, and by using solid spacers to reduce the storage chamber's free volume.

Jang, J., Waite, W.F., Stern, L.A., Collett, T.S., Kumar, P., 2019. Physical property characteristics of gas hydrate-bearing reservoir and associated seal sediments collected during NGHP-02 in the Krishna-Godavari Basin, in the offshore of India. Marine and Petroleum Geology 108, 249-271.


India's National Gas Hydrate Program Expedition 02 (NGHP-02) was conducted to better understand geologic controls on gas hydrate occurrence and morphology, targeting coarse-grained sediments along the lower continental slope offshore eastern India. This study combines seismic, logging-while-drilling data, and a petroleum system approach to provide a regional geologic and lithologic context for: 1) gas hydrate morphology and distribution, and 2) effects of fine-grained sediments (clays and other grains smaller than 63 μm) on gas production in NGHP-02 Area B in the Krishna-Godavari Basin. Area B seismic data show a buried anticline/syncline structure with strong reflectors, R1 and R2, that delineate two of the five lithologic units: Unit I (shallowest), II (R1), III, IV (R2) and V (below the bas of gas hydrate stability). Throughout Area B, gas hydrate morphology depends on its placement within these units. Specifically, core- and grain-scale measurements indicate fines content exerts a primary control on the gas hydrate distribution and morphology. Units I, II and III are generally fine-grained. On the anticline crest, these units host primarily grain-displacing gas hydrate veins linked to pore-occupying gas hydrate in thin, localized, coarser-grained deposits. Diatoms in Unit III increase porosity with depth, reaching ∼70% where it contacts Unit IV, the gas hydrate reservoir associated with reflector R2. The Unit III lithology and porosity allow fluid and dissolved-phase methane to escape Unit IV and form gas hydrate in the fine-grained overburden. Within Unit IV, fine-grained layers are interbedded with coarser-grained gas hydrate reservoir sands, and the fines content even in the sands is high enough to impact hydraulic and mechanical properties during gas production. Fluid motion during gas production can mobilize fines, which can then clog pore throats, limiting production rates. Pore-water freshening during gas hydrate dissociation can increase fines mobilization, particularly given the smectite identified in the fine-grained interbeds.



The efficiency of the dimethyl ether (DME) enhanced oil recovery (EOR) technique in a fractured chalk reservoir core plug was investigated. The coreflood experiment showed that DME EOR could lead to 44.2% additional oil recovery, amounting to 80.6% of the ultimate oil recovery. A comprehensive set of laboratory experiments, including density measurements of miscible fluids, DME-induced oil swelling factor, and partition coefficient of DME between the aqueous and oleic phase, were performed. The experimental results show that the partition coefficient of DME for the mixture of DME–brine–oil can reach up to 18.3. The oil swelling factor for such a system can reach up to 2.7 under realistic reservoir conditions. Comparing this data set to the available data for other mutually soluble solvent-based EOR techniques shows that the oil swelling caused by DME is far stronger than for other common solvents. Due to the strong partitioning of DME between the phases, the DME from the DME–brine solution rapidly partitions into the bypassed oil in the low permeability matrix, which leads to strong oil swelling and production.



The nanometer-scale architecture of organic matter (OM) and associated pores in highly mature gas shales from the lower Silurian Longmaxi Formation in the upper Yangtze platform of south China were investigated using field emission scanning electron microscopy (SEM), focused ion beam SEM, and low-pressure gas (N2 and CO2) adsorption bulk pore characterization. The Longmaxi shale comprises fine-grained siliciclastic rocks deposited in a marine shelf environment, which was dominated by quartz and clay minerals. Four porous OM types were found in the Longmaxi shale on the basis of the chemical composition and spatial occurrence of OM, including (1) isolated original OM particles, (2) OM–clay mineral complexes, (3) OM–heavy mineral complexes, and (4) secondary migrated bituminous OM. The pores in the particulate OM are not homogeneously distributed, and the processes leading to different pores depend on the specific OM type. The nature of OM-hosted pores is a result of several factors, such as primary porous kerogen, mechanical

compaction, organic–inorganic interactions, gaseous and liquid hydrocarbon generation, retention, and expulsion. Pore volumes and specific surface areas of the Longmaxi shale derived from low-pressure N2 and CO2 adsorption experiments reveal positive linear relationships with total organic carbon contents, which indicates that the pore systems in the highly mature Longmaxi shale are dominated by OM-hosted pores. Additionally, the OM-hosted pores appear connected compared to pores in the mineral matrix. Therefore, the OM-hosted pore systems offer the preferential storage space and primary migration pathways for natural gas in the Longmaxi shale reservoir.

Jiang, T., Wang, D., Meng, B., Chi, J., Laudon, H., Liu, J., 2020. The concentrations and characteristics of dissolved organic matter in high-latitude lakes determine its ambient reducing capacity. Water Research 169, 115217.


The reducing capacity (RC) of natural organic matter plays an important role in the carbon cycle and biogeochemical fates of environmental contaminants in the aquatic system. However, the electron donation potentials of dissolved organic matter (DOM) from high-latitude lakes are still uncertain. In this study, we collected DOM samples from high-latitude lakes across the Arctic and boreal regions in Sweden and Norway to investigate the effects of the DOM concentration and characteristics on its ambient reducing capacity (ARC). Mercury (Hg(II)) abiotic reduction in darkness was used to determine the ARC. The results showed that the DOM in Arctic lakes is less terrestrial-dominant than in reference sites (i.e., forest lakes). Between the two categories of Arctic lakes, tundra lakes are more terrestrial-influenced compared to mountain lakes. Additionally, terrestrial-originated DOM is a main controlling factor for enhancing the ambient reducing capacity, whereas the DOM concentration, i.e., dissolved organic carbon (DOC), resulted in variations in the Hg/DOC ratios that also cause the variations of the observed ARC values. Thus, comparisons of the ARC values can be conducted while oxidant/DOC ratios are kept the same and reported through the method using heavy metals as a chemical probe. After correction for Hg/DOC ratio interference, the ambient reducing capacity of DOM followed the order: boreal forest lakes > Arctic tundra lakes > Arctic mountain lakes. This study highlights that the DOM concentration should also be considered when estimating the ARC as compared to the previous that mainly focusing on the properties of DOM such as its origins. As climate change is projected to be severe in high latitudes, this study demonstrates a significant connection between aquatic DOM geochemical reactivity and terrestrial inputs, which is crucial for a better prediction of the role of DOM in high-latitude lakes in the context of climate change.

Jiang, Y., Liu, X., Fu, Y., Chen, H., Zhang, H., Yan, J., Chen, C., Gu, Y., 2019. Evaluation of effective porosity in marine shale reservoir, western Chongqing Acta Petrolei Sinica 40, 1233-1243 http://www.syxb-cps.com.cn/EN/abstract/abstract5768.shtml

Based on the Nuclear Magnetic Resonance (NMR)response characteristics of capillary bond water, clay bound water, clay hydration water and kerogen in shale reservoir, this study carries out an evaluation research on the effective porosity in shale. The samples were obtained from the shale reservoir buried deeper than 3 500 m in Well Z202 and Z201, on which a NMR experiment was performed after gradient centrifugation and gradual drying of the shale samples. The results indicate that the T2cutoff of capillary bound water, clay bound water and basement signal is within the range of 0.98-1.08 ms, 0.25-0.55 ms and 0.12-0.20 ms, respectively. The three T2cutoff values decrease gradually, corresponding to the mobile water saturation, capillary bond water saturation and clay bound water saturation of 29.72% -48.12%, 10.25% -20.19% and 12.97% -15.68%, respectively. The T1-T2 Spectra for the core dried at 200 reveal that disconnected pores exist in shale. The pore system of shale ℃reservoir has been subdivided using the quantitative research method. Then the mean T2cutoff value of lower limit of effective porosity has been determined as 0.4 ms, corresponding to the lower limit of pore size (4.25 nm). On this basis, this study has established a serious of techniques and methods for evaluating effective shale reservoir, so as to identify the pore fluid type, subdivide the pore system, evaluate the pore porosity, and determine the lower limit of effective pore size.

Jiang, Z., Shi, M., Shi, L., 2020. Degradation of organic contaminants and steel corrosion by the dissimilatory metal-reducing microorganisms Shewanella and Geobacter spp. International Biodeterioration & Biodegradation 147, 104842.


Shewanella and Geobacter are the two genera of dissimilatory metal-reducing microorganisms that can couple intracellular oxidation of organic matter to extracellular reduction of oxidized metal ions, such as solid-phase iron (Fe(III)) and manganese (Mn(IV) (hydr)oxides. To transfer electrons extracellularly, both Shewanella and Geobacter spp. possess pathways that transfer electrons from the quinone/quinol pool in the cytoplasmic membrane, across the cell envelope to the extracellular Fe(III) and Mn(IV) (hydr)oxides. In addition, Geobacter spp. use electrically conductive pili and/or filaments that consist of multiheme c-type cytochromes for long-distance electron transfer to Fe(III) and Mn(IV) (hydr)oxides and other electron acceptors. Furthermore, the Fenton reaction driven by Shewanella oneidensis MR-1 can be used to degrade a variety of organic contaminants. Some Geobacter spp., such as Geobacter metallireducens GS-15, couple oxidative degradation of benzine, phenol and other aromatic contaminants to Fe(III) reduction. Moreover, other Geobacter spp., such as G. loveleyi SZ, also couple oxidation of organic matter to reductive dichlorination of organohalide contaminants. Finally, under anoxic condition, Shewanella and Geobacter spp. corrode carbon steel by direct oxidation. This review focuses on our current understandings of extracellular electron transfer mechanisms of as well as degradation of organic contaminants and steel corrosion by Shewanella and Geobacter spp.

Jimenez, B.A.L., Aguilera, R., 2019. Physics-based fluid-flow modeling of liquids-rich shale reservoirs using a 3D three-phase multiporosity numerical-simulation model. SPE Reservoir Evaluation & Engineering 22, 1501-1526.

https://doi.org/10.2118/191459-PA

Production from liquids-rich shale reservoirs in the US and Canada has increased significantly during the past few years. However, a rigorous understanding of shale rocks and fluid flow through them is still limited and remains a challenge. Thus, the objective of our research is developing a 3D physics-based model for simulating fluid flow through these types of multiporosity rocks. This is important given the recent spread of these types of reservoirs throughout the world.

Simulation of liquids-rich shale reservoirs is performed with the construction of an original fully implicit 3D multiphase modified black-oil finite-difference numerical formulation, which uses a multiporosity approach as well as diffusion from solid kerogen. The multiporosity system includes adsorbed porosity, organic porosity, inorganic porosity, natural-fracture porosity, and hydraulic-fracture porosity. A numerical model is developed with capabilities to handle dissolved gas in the solid part of the organic matter, adsorption/desorption from the organic pore walls, viscous- and non-Darcy-flow mechanisms (slip flow and Knudsen diffusion), and stress-dependent properties of natural and hydraulic fractures.

Examples of simulated results are presented as crossplots of pressure, production rates, and cumulative production vs. time. These plots are used to show the contributions of free gas, adsorbed gas, and dissolved gas to fluid production from liquids-rich shale reservoirs. Results indicate that both desorption and gas diffusion positively affect shale performance. Simulation results demonstrate that not taking into account desorption and diffusion from solid kerogen leads to underestimating production from liquids-rich shale reservoirs. Furthermore, the simulation study shows that long periods of time are required for the effects of these two mechanisms to be manifested. This helps to explain why shales have been produced over long periods of time (several decades), such as in the case of Devonian wells in the Appalachian Basin.

The type of 3D simulation model for multiporosity liquids-rich shale reservoirs developed in this paper is not currently available in the literature. The approach implemented in this paper provides a novel and important foundation for simulating complex shale reservoirs.

Johnson, J.J., Olin, J.A., Polito, M.J., 2019. A multi-biomarker approach supports the use of compound-specific stable isotope analysis of amino acids to quantify basal carbon source use in a salt marsh consumer. Rapid Communications in Mass Spectrometry 33, 1781-1791.


Rationale: Determining the flow of energy from primary producers to higher trophic levels in complex systems remains an important task for ecologists. Biomarkers can be used to trace carbon or energy sources contributing to an organism's tissues. However, different biomarkers vary in their ability to trace carbon sources based on how faithfully they transfer between trophic levels. Comparing emerging biomarker techniques with more commonly used techniques can demonstrate the relative efficacy of each in specific systems.

Methods: Two common biomarker techniques, fatty acid analysis (FAA) and bulk stable isotope analysis (SIA), and one emerging biomarker technique, compound‐specific stable isotope analysis of amino acids (CSIA‐AA), were compared to assess their ability to characterize and quantify basal carbon sources supporting the seaside sparrow (Ammodramus maritimus), a common salt marsh species. Herbivorous insect and deposit‐feeding fiddler crab biomarker values were analyzed as proxies of major terrestrial and aquatic basal carbon sources, respectively.

Results: All three biomarker techniques indicated that both terrestrial and aquatic carbon sources were important to seaside sparrows. However, FAA could only be evaluated qualitatively, due to a currently limited understanding of trophic modification of fatty acids between primary producer and this consumer's tissues. Quantitative stable isotope (SIA or CSIA‐AA) mixing models predicted nearly equal contributions of terrestrial and aquatic carbon sources supporting seaside sparrows, yet estimates based on CSIA‐AA had greater precision.

Conclusions: These findings support the use of CSIA‐AA as an emerging tool to quantify the relative importance of basal carbon sources in salt marsh consumers. Integrating multiple biomarker techniques, with their differing benefits and limitations, will help to constrain models of carbon and energy flow in future ecosystem studies.

Jones, R.K., Piper, P.J., Wood, R., Nguyen, A.T., Oxenham, M.F., 2019. The Neolithic transition in Vietnam: Assessing evidence for early pig management and domesticated dog. Journal of Archaeological Science: Reports 28, 102042.


The onset of Neolithic food-producing cultures during the Mid Holocene in Southeast Asia (SEA) constituted major social and demographic change. In northern Vietnam, the Late Holocene site of Man Bac has been argued to capture this shift in population and material culture. This paper provides an updated faunal record of Man Bac and assesses the evidence for dog domestication and pig management at the site. Using a mixed method approach combining morphometric analyses, cluster analysis, mortality profiles, and body part representation, dogs are confidentially determined to be domesticated, and pigs are argued to represent an early management strategy. Direct 14C dating on select pig and dog elements provide the current earliest date for these domesticated animals in northern Vietnam and reflects the early expansion of farming communities into Mainland Southeast Asia (MSEA).

Jones, S.M., Prave, A.R., Raub, T.D., Cloutier, J., Stüeken, E.E., Rose, C.V., Linnekogel, S., Nazarov, K., 2020. A marine origin for the late Mesoproterozoic Copper Harbor and Nonesuch Formations of the Midcontinent Rift of Laurentia. Precambrian Research 336, 105510.


The c. 1.1 Ga Copper Harbor and Nonesuch Formations of the Keweenawan Supergroup exposed along the Canadian-United States shorelines of Lake Superior are part of the surface exposures of the Laurentian Midcontinent Rift. These units have long been considered non-marine in origin and have figured prominently in

ideas regarding the evolution of microbial life and the redox conditions of Earth’s ocean-atmosphere system at the close of Mesoproterozoic time. However, these rocks also host hydrothermal metal deposits, the emplacement of which may have compromised primary geochemical signals that are used to underpin those ideas. Here we highlight new sedimentological observations to provide an independent framework for assessing the depositional setting and geochemistry of those strata. We show that the totality of sedimentological features leads to the conclusion that parts of the upper Copper Harbor Formation and the entirety of the Nonesuch Formation were deposited along tide- and wave-influenced shorelines and in shallow-marine settings under evaporitic conditions. Evidence for this interpretation includes the abundance of flaser, wavy, linsen and pinstripe bedding, ubiquity of reactivation surfaces and mud drapes associated with all ripple forms, superposed sets of ripple cross-lamination showing bimodal (herring-bone) sediment transport directions, desiccation cracks and metre-scale hummocky cross-stratification. Further, evaporite fabrics and pseudomorphs after gypsum in the upper 200 m of the Copper Harbor Formation and in numerous stratigraphic positions within the Nonesuch Formation indicate that the water body was saline, not fresh. The emerging palaeogeographic image is one of a large, shallow-marine embayment with fringing sabkha-like shorelines. Ideas about late Mesoproterozoic biospheric evolution and Earth’s surface redox and oxygenation that rely on the Nonesuch Formation and Copper Harbor stromatolites having been deposited within a lacustrine setting require reassessment.

Jordan, S.F., Rammu, H., Zheludev, I.N., Hartley, A.M., Maréchal, A., Lane, N., 2019. Promotion of protocell self-assembly from mixed amphiphiles at the origin of life. Nature Ecology & Evolution 3, 1705-1714.

https://doi.org/10.1038/s41559-019-1015-y

Vesicles formed from single-chain amphiphiles (SCAs) such as fatty acids probably played an important role in the origin of life. A major criticism of the hypothesis that life arose in an early ocean hydrothermal environment is that hot temperatures, large pH gradients, high salinity and abundant divalent cations should preclude vesicle formation. However, these arguments are based on model vesicles using 1–3 SCAs, even though Fischer–Tropsch-type synthesis under hydrothermal conditions produces a wide array of fatty acids and 1-alkanols, including abundant C10–C15 compounds. Here, we show that mixtures of these C10–C15 SCAs form vesicles in aqueous solutions between pH ~6.5 and >12 at modern seawater concentrations of NaCl, Mg2+ and Ca2+. Adding C10 isoprenoids improves vesicle stability even further. Vesicles form most readily at temperatures of ~70 °C and require salinity and strongly alkaline conditions to self-assemble. Thus, alkaline hydrothermal conditions not only permit protocell formation at the origin of life but actively favour it.

Joshi, A.K., Sain, K., Pandey, L., 2019. Gas hydrate saturation and reservoir characterization at sites NGHP-02-17 and NGHP-02-19, Krishna Godavari Basin, eastern margin of India. Marine and Petroleum Geology 108, 595-608.


We have characterized the gas hydrate reservoir at Sites NGHP-02-17 and NGHP-02-19 based on isotropic and anisotropic velocity modeling by utilizing both the wireline (WL) and logging-while-drilling (LWD) data independently. The isotropic study is carried out using the simplified three phase Biot equation (STPBE) with density derived porosity and calculated bulk density of sediments as inputs. The anisotropic study uses the transverse isotropic theory for laminated media by considering a layered reservoir model composed of two components: (i) fractures filled with 100% gas hydrates and (ii) isotropic medium composed of water-saturated sediments. In the anisotropic velocity modeling, the reservoir is modeled by incorporating fractures with varying dip angles from 0° to 90°. We estimated gas hydrate saturations using isotropic and anisotropic velocity analysis at both Sites NGHP-02-17 and NGHP-02-19. In both the cases the LWD data derived isotropic model yielded, what appears to be the most accurate values, an average saturation of 45.8% in the high velocity interval between 269 and 285.5 mbsf at Site NGHP-02-17 and 33.8% in the high velocity interval between 306 and 312 mbsf in NGHP-02-19.

Kaal, J., Martín Seijo, M., Oliveira, C., Wagner-Wysiecka, E., McCoy, V.E., Solórzano Kraemer, M.M., Kerner, A., Wenig, P., Mayo, C., Mayo, J., 2020. Golden artefacts, resin figurines, body adhesives and tomb sediments

from the pre-Columbian burial site El Caño (Gran Coclé, Panamá): Tracing organic contents using molecular archaeometry. Journal of Archaeological Science 113, 105045.


This research aimed to determine the origin of organic residues from funerary contexts in the El Caño settlement (Gran Coclé area, Panamá, Central America) by means of multiple molecular probing techniques (GC-MS of organic solvent extracts and pyrolysis-GC-MS, THM-GC-MS and FTIR of solid samples). The samples include particles of precious resin figurines, fillings of golden objects, tomb sediments, plant exudates from extant plants (reference collection) and other reference materials (amber). The labdane diterpene fingerprints (eperuic, iso-ozic, copalic and kolavenic acids and derivatives) of the resin figurines, a resinous bead and several other samples, suggest that they were composed primarily of Hymenaea resin. Besides traditional interpretation approaches (visual comparison of chromatograms and relative proportions data), we used a novel OpenChrom® application that resolves complex pyrolysis chromatograms by screening data from archaeological samples for marker products defined on the basis of a reference collection (ChromIdent). ChromIdent confirmed the Hymenaea origin of many samples and also Burseraceae resin was identified in some samples, which is present as a minor ingredient in resin figurines (indicative of mixing practices) and as the dominant resin in tomb sediment that had been in contact with the corpses (indicating balsaming practices). The degree of polymerization of the Hymenaea resin was higher than for extant resin but diagenetic alteration (especially condensation of cyclic moieties) was much smaller than for amber, implying that the manufacturers used resin (or copal), not amber. These results were confirmed by FTIR, which allowed identification of non-fossil Hymenaea resin as the main constituent of one of the resin figurines. Several golden object infillings contained wax derivatives, probably beeswax, accompanied by various types of plant resin, which may well indicate the use of meliponines' cerumen for manufacturing (lost-wax casting). The findings highlight the potential of complementary molecular techniques to resolve questions on materials and manufacturing of archaeological artefacts, and the need for cross-comparison of molecular and ethnographic information in the study of archaeobotanical remains and the processes involved in their management.

Kadnikov, V.V., Savvichev, A.S., Mardanov, A.V., Beletsky, A.V., Merkel, A.Y., Ravin, N.V., Pimenov, N.V., 2019. Microbial communities involved in the methane cycle in the near-bottom water layer and sediments of the meromictic subarctic Lake Svetloe. Antonie van Leeuwenhoek 112, 1801-1814.

https://doi.org/10.1007/s10482-019-01308-1

Although arctic and subarctic lakes are important sources of methane, the emission of which will increase due to the melting of permafrost, the processes related to the methane cycle in such environments are far from being comprehensively understood. Here we studied the microbial communities in the near-bottom water layer and sediments of the meromictic subarctic Lake Svetloe using high-throughput sequencing of the 16S rRNA and methyl coenzyme M reductase subunit A genes. Hydrogenotrophic methanogens of the order Methanomicrobiales were abundant, both in the water column and in sediments, while the share of acetoclastic Methanosaetaceae decreased with the depth of sediments. Members of the Methanomassiliicoccales order were absent in the water but abundant in the deep sediments. Archaea known to perform anaerobic oxidation of methane were not found. The bacterial component of the microbial community in the bottom water layer included oxygenic (Cyanobacteria) and anoxygenic (Chlorobi) phototrophs, aerobic Type I methanotrophs, methylotrophs, syntrophs, and various organotrophs. In deeper sediments the diversity of the microbial community decreased, and it became dominated by methanogenic archaea and the members of the Bathyarchaeota, Chloroflexi and Deltaproteobacteria. This study shows that the sediments of a subarctic meromictic lake contain a taxonomically and metabolically diverse community potentially capable of complete mineralization of organic matter.

Käfer, U., Gröger, T., Rohbogner, C.J., Struckmeier, D., Saraji-Bozorgzad, M.R., Wilharm, T., Zimmermann, R., 2019. Detailed chemical characterization of bunker fuels by high-resolution time-of-flight mass spectrometry hyphenated to GC × GC and thermal analysis. Energy & Fuels 33, 10745-10755.


On January 1, 2020, new International Maritime Organization (IMO) legislation will reduce the maximum sulfur content for marine fuels outside of sulfur emission control areas (SECA) from now 3.50% (m/m) to 0.50% (m/m) to lower the emission of SOx. In order to enable a smooth transition to the new-generation fuels and to cope with a widely diversified spectrum of heavy fuel oils, a comprehensive chemical description of such bunker fuels will become more important to investigate differences which may cause incompatibility with current engines or to avoid a negative impact for the storage stability. Comprehensive two-dimensional gas chromatography with mass-spectrometric detection (GC × GC-MS) has become one of the most potent analytical methods for detailed analysis of hydrocarbon composition in complex petroleum fractions. However, matrices that contain significant amounts of less- or nonvolatile constituents, such as marine fuels, cannot entirely be targeted by gas chromatography alone. In order to extend the application range of a GC × GC high-resolution time-of-flight mass spectrometry platform (GC × GC-HRTOFMS), we applied and compared thermogravimetric analysis (TGA-HRTOFMS) and direct inlet probe (DIP-HRTOFMS) as additional thermal sample introduction techniques. In this study, we investigated five different marine fuels with GC × GC-, DIP-, and TGA-HRTOFMS to analyze volatile as well as residual compounds. Since each of the deployed techniques showed unique advantages and possibilities, the complementarity of the combined approach is demonstrated. The combination of GC × GC-, DIP-, and TGA-HRTOFMS data enabled the generation of comprehensive chemical fingerprints for differentiation and chemical classification.

Kaiser, J., Wasmund, N., Kahru, M., Wittenborn, A.K., Hansen, R., Häusler, K., Moros, M., Schulz-Bull, D., Arz, H.W., 2019. Reconstructing N2-fixing cyanobacterial blooms in the Baltic Sea beyond observations using 6- and 7-methylheptadecanes in sediments as specific biomarkers. Biogeosciences Discussions 2019, 1-24.


Summer cyanobacterial blooms represent a threat for the Baltic Sea ecosystem, causing deoxygenation of the bottom water and the spread of the so-called dead zones. The time history of the Baltic Sea cyanobacterial blooms is known from in situ and satellite observations since the early 1980s, but still not well understood. By comparing both weekly-resolved trap sediments and a well-dated sediment core from the Eastern Gotland Basin with monitoring and satellite cyanobacterial data of the last ca. 35 years, it is shown here that 6- and 7-methylheptadecane lipids (expressed as 6+7Me-C17:0) are robust semi-quantitative biomarkers for diazotrophic cyanobacteria, and likely mainly for Nodularia spumigena. Using this organic proxy, it was thus possible to reconstruct the history of cyanobacterial blooms beyond the observational period with a resolution of 2–4 years since 1860. Cyanobacteria were constantly present, but in relatively low abundance until 1920, when they started to alternate between periods with high and low abundance. Interestingly, there seems to be no significant increase in cyanobacterial abundance in the 1950s, when eutrophication and deoxygenation of the Baltic Sea increased considerably. Decadal to multi-decadal fluctuations are likely rather related to variability in the Baltic Sea surface temperature and, ultimately, to the Atlantic Multidecadal Oscillation. A 7000 years long 6+7Me-C17:0 record from the Bothnian Sea also suggests a relationship with the mean summer temperature in the Baltic Sea region, but at a multi-centennial to multi-millennial timescale. The intensity of the cyanobacterial blooms in the Baltic Sea is thus likely mainly related to natural processes such as temperature variability, at least at a multi-decadal to multi-millennial timescale.

Kallscheuer, N., Moreira, C., Airs, R., Llewellyn, C.A., Wiegand, S., Jogler, C., Lage, O.M., 2019. Pink- and orange-pigmented Planctomycetes produce saproxanthin-type carotenoids including a rare C45 carotenoid. Environmental Microbiology Reports 11, 741-748.

https://doi.org/10.1111/1758-2229.12796

Planctomycetes are ubiquitous and environmentally important Gram‐negative aquatic bacteria with key roles in global carbon and nitrogen cycles. Many planctomycetal species have a pink or orange colour and have been suggested to produce carotenoids. Potential applications as food colorants or anti‐oxidants have been proposed. Hitherto, the planctomycetal metabolism is largely unexplored and the strain pigmentation has not been explored. For a holistic view of the complex planctomycetal physiology, we analysed carotenoid profiles of the pink‐pigmented strain Rhodopirellula rubra LF2T and of the orange strain Rubinisphaera brasiliensis Gr7.

During LC–MS/MS analysis of culture extracts, we could identify three saproxanthin‐type carotenoids including a rare C45 carotenoid. These compounds, saproxanthin, dehydroflexixanthin and 2′‐isopentenyldehydrosaproxanthin, derive from the common carotenoid precursor lycopene and are characterized by related end groups, namely a 3‐hydroxylated β‐carotene‐like cyclohexene ring as one end group and simple hydration on the other end of the molecule. Based on the observed molecule structure we present putative pathways for their biosynthesis. Results support Planctomycetes as a promising, yet mostly untapped source of carotenoids.

Kang, Y., Schneider, B.B., Bedford, L., Covey, T.R., 2019. Design characteristics to eliminate the need for parameter optimization in nanoflow ESI-MS. Journal of The American Society for Mass Spectrometry 30, 2347-2357.

https://doi.org/10.1007/s13361-019-02301-8

The sampling efficiency in electrospray ionization-mass spectrometry (ESI-MS) can be improved by decreasing the liquid flow rate to the nanoflow regime, where it is possible to draw a large fraction of the ESI plume into the mass spectrometer. This mode of operation is typically more difficult than ESI-MS at higher flow rates because it requires careful optimization of a number of parameters to achieve optimal sampling efficiency. In this work, we screened the relative impact on signal intensity and spray stability of factors that included sprayer position, spray electrode protrusion, sprayer tip shape, spray angle relative to the MS inlet, nebulizer gas flow rate, ESI potential, and means for generating the electric field to initiate electrospray. Based on the screening results, we explore the possibility of providing fixed optimal values for many of the key source parameters to eliminate much of the tuning that is required for conventional nanoflow sources. This approach has potential to greatly simplify nanoflow ESI-MS, while providing optimized sensitivity, stability, and robustness, with decreased variability between analyses.

Kappelmann, J., Beyß, M., Nöh, K., Noack, S., 2019. Separation of 13C- and 15N-isotopologues of amino acids with a primary amine without mass resolution by means of O-phthalaldehyde derivatization and collision induced dissociation. Analytical Chemistry 91, 13407-13417.


Computational and experimental advances of recent years have culminated in establishing 13C-Metabolic Flux Analysis (13C-MFA) as a routine methodology to unravel the fluxome. As the acronym suggests, 13C-MFA has relied on the relative abundance of 13C-isotopes in metabolites for flux inference, most commonly measured by mass spectrometry. In this manuscript we expand the scope of labeling measurements to the case of simultaneous 13C- and 15N-labeling of amino acids. Analytically, the separation of isotopologues of this metabolite class can only be achieved at resolving power beyond 65,000. In this manuscript we harvest an overlooked property of the collision induced dissociation of amino acid adducts to discern 13C- and 15N- isotopologues of amino acids with a primary amine without separating them in the m/z domain.

Karabeyoğlu, A.U., Özkan-Altıner, S., Altıner, D., 2019. Quantitative analysis of planktonic foraminifera across the Cretaceous-Paleogene transition and observations on the extinction horizon, Haymana Basin, Turkey. Cretaceous Research 104, 104169.


The Haymana Basin, Turkey, hosts complete record of sedimentation across the Cretaceous-Paleogene (K-Pg) boundary. To examine the K-Pg boundary transition and delineate the bioevents, two consecutive sections (UH and UKHB) were measured and sampled at high resolution. Three biozones were established: Plummerita hantkeninoides, P0 and Pα. A detailed quantitative study on planktonic foraminifera was carried out for the P. hantkeninoides and the P0 zones for 63–150 μm and >150 μm size fractions. Results show dominance of ecological generalists with small, simple tests over ecological specialists with large, robust, ornamented morphologies. Heterohelicids are the most dominant group on both size fractions throughout the late Maastrichtian, however right after the K-Pg boundary Guembelitria cretacea blooms and dominates the planktonic foraminiferal assemblage in early Danian P0 Zone. The K-Pg boundary characterizes itself as 2–3 mm thick reddish oxidized layer and its transition reveals a series of events: A rapid change in sedimentation from Maastrichtian mudstones to Danian marls. A sudden annihilation of large, ornamented ecological specialists (e.g., Globotruncana, Rugoglobigerina, Planoglobulina) right at the reddish layer (even though quantitative study revealed that there is a systematic reduction in the foraminiferal species richness throughout the P. hantkeninoides Zone). Spikes of calcareous dinoflagellate Thoracosphaera and fecal pellets right after the K-Pg boundary in the Danian P0 Zone. Anomalous increase in CaO rich spherules and amorphous grains coupled with barite crystals right at the K-Pg boundary layer. Paleobathymetric calculations also revealed approximately 400 m paleodepth for the study area corresponding the upper bathyal zone.

Kato, A., Konno, Y., Yoneda, J., Kida, M., Oshima, M., Jin, Y., Nagao, J., Tenma, N., 2019. Evaluation of failure modes and undrained shear strength by cone penetrometer for Natural Gas hydrate-bearing pressure-core sediment samples recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 502-511.


Compressional wave velocity measurements and cone penetration tests were carried out for pressure cores recovered from the Krishna–Godavari Basin off the eastern coast of India, using an instrumented pressure testing chamber constructed by the Japanese National Institute of Advanced Industrial Science and Technology. For pressure cores with high gas hydrate saturations (Sh) and exhibited high compressional wave velocities also display a high loading force that resulted in tensile failure. A pressure core sample with low compressional wave velocities and low gas hydrate saturations led to a low loading force, which resulted in radial shear. The cone factor connecting the cone resistance and the undrained shear strength, Nk, was estimated using cone penetration testing and the uniaxial compressional results. We estimated its value as Nk = 45 by using a uniaxial compression loading speed of 0.01%/min and a cone insertion loading speed of 0.25 mm/s. Undrained shear strengths, estimated from cone penetration results using Nk = 45, were assumed to be equal to the tensile strengths between hydrate-hydrate and hydrate-particle interface when Sh is less than 50% and increases when Sh is more than 50% assuming that gas hydrate morphology was matrix supporting.

Kayukova, G.P., Mikhailova, A.N., Vandyukova, I.I., 2020. Features of the elemental, structural-group, and microelement composition of asphaltenes from natural bitumens of the Permian deposits of Tatarstan. Petroleum Science and Technology 38, 18-23.

https://doi.org/10.1080/10916466.2019.1655444

Using a complex of physical and chemical methods studied features of the elemental, structural-group, and microelement composition of natural bitumen asphaltenes extracted from bituminous rocks of Tatarstan?s Permian deposits. It is an investigated interconnection of value changes of spectral parameters (of aromaticity, oxidation, and aliphatic) characterizing of structural-group composition of original bitumen and asphaltenes. The features of the microelement composition of asphaltenes of bitumen of various types were also revealed.

Kelley, C.A., Bebout, B.M., Chanton, J.P., Detweiler, A.M., Frisbee, A., Nicholson, B.E., Poole, J., Tazaz, A., Winkler, C., 2019. The effect of bacterial sulfate reduction inhibition on the production and stable isotopic composition of methane in hypersaline environments. Aquatic Geochemistry 25, 237-251.

https://doi.org/10.1007/s10498-019-09362-x

The aim of this research was to investigate the competition between methanogens and sulfate-reducing bacteria in hypersaline environments. Samples of photosynthetic microbial mats, both soft mats (salinities of 55–126 ppt) and gypsum-hosted endoevaporite mats (salinities of 77–320 ppt), were obtained from hypersaline environments in California, USA, Mexico and Chile. Methane production was determined from the increase in headspace methane concentration within incubation vials containing mat samples. At the end of the incubation period, the δ13C values of produced methane were measured. Soft microbial mat vials containing molybdate, a specific inhibitor of bacterial sulfate reduction, exhibited dramatically higher methane production rates and higher (enriched in 13C) methane δ13C values than the controls. This suggests that the inhibition of sulfate reduction allowed the methanogens at these sites to use the competitive substrates (H2 and/or acetate) made available. Further, the higher δ13C values of the produced methane suggest that substrates (both competitive and non-competitive) were used to near completion. At the endoevaporite sites, which have much higher salinities than the soft mat sites, methane production was not significantly different and the methane δ13C values either remained the same or decreased (depleted in 13C) with added molybdate. We suggest that substrate availability increased enough to allow for somewhat greater isotopic fractionation resulting in the lower methane δ13C values that were observed, but not enough to significantly increase measured production rates. Where no changes in either methane production rates or δ13C values occurred, we hypothesize that salinity itself was inhibiting sulfate reduction and thus controlling microbe populations and rates of metabolism.



The Bight Basin along the southern margin of Australia represents one of Australia's most prospective deep-water frontier hydrocarbon exploration regions, however its 15 km-thick sedimentary succession remains largely untested. Whilst there is some evidence of oil from shows, fluid inclusions and natural strandings of asphaltite along the basin margin, it is unclear if any hydrocarbons were generated in the deep-water Ceduna Sub-basin. Fluid inclusions offer a unique method to test for petroleum migration that would otherwise remain hidden and a study, using CSIRO's Grains with Oil Inclusion (GOI™) technique, was undertaken on Gnarlyknots-1A along with other historic exploration wells. With the exception of Jerboa-1, in the Eyre Sub-basin, the GOI

results (<0.1% up to 1.1%) both reaffirm evidence for hydrocarbon migration along the shallow-water shelf edges and, most significantly, provide new insight on the petroleum potential of the deep-water Ceduna sub-basin. Anomalous occurrences of oil and some gas-condensate assemblages in the primary Coniacian drilling target of Gnarlyknots-1A, as well as Turonian and Santonian intervals, indicate multiple phases of hydrocarbon migration trapped within micro-fractures of detrital grains. This fluid inclusion evidence provides the first consistent indication of a working, liquids-prone, petroleum system in this deep-water part of the basin.

Kerraouch, I., Ebert, S., Patzek, M., Bischoff, A., Zolensky, M.E., Pack, A., Schmitt-Kopplin, P., Belhai, D., Bendaoud, A., Le, L., 2019. A light, chondritic xenolith in the Murchison (CM) chondrite – Formation by fluid-assisted percolation during metasomatism? Geochemistry 79, 125518.


The main mineralogical characteristics of a large light-colored clast within the Murchison CM breccia are discussed in detail including data on the mineralogy, bulk chemistry, organics, and oxygen isotopes. Petrographic study shows that the white clast consists of two areas with different granoblastic textures: (1) a coarse-grained (average grain size: ˜200 μm) and (2) a fine-grained lithology (average grain-size: ˜20 μm). The Fa-content of olivine in the clast is the same as Fa within olivine from Rumuruti (R) chondrites (Fa: ˜38 mol%); however, the concentrations of the elements Ni and Ca in olivine are significantly different. The fragment also contains Ca-rich pyroxene, Ãn30-38-plagioclase/maskelynite, Cr-rich spinel, several sulfide phases, a nepheline-normative glass, and traces of merrillite and metal. The occurrence of maskelynite and nepheline-normative amorphous phase in restricted areas of the well-recrystallized rock may indicate remarkable P-T-excursions during shock metamorphism. The O-isotope composition of the clast falls below the terrestrial fractionation line (TFL), lying in the field of CM chondrites and is significantly different from data for bulk R chondrites. The study of the soluble organic matter revealed a highly-oxidized carbon chemistry and organomagnesium compounds reflecting high temperature and pressure processes.

Kerudin, A., Müller, R., Buckberry, J., Knüsel, C.J., Brown, T.A., 2019. Ancient Mycobacterium leprae genomes from the mediaeval sites of Chichester and Raunds in England. Journal of Archaeological Science 112, 105035.


We examined six skeletons from mediaeval contexts from two sites in England for the presence of Mycobacterium leprae DNA, each of the skeletons displaying osteological indicators of leprosy. Polymerase chain reactions directed at the species-specific RLEP multicopy sequence produced positive results with three skeletons, these being among those with the clearest osteological signs of leprosy. Following in-solution hybridization capture, sufficient sequence reads were obtained to cover >70% of the M. leprae genomes from these three skeletons, with a mean read depth of 4–10×. Two skeletons from a mediaeval hospital in Chichester, UK, dating to the 14th–17th centuries AD, contained M. leprae strains of subtype 3I, which has previously been reported in mediaeval England. The third skeleton, from a churchyard cemetery at Raunds Furnells, UK, dating to the 10th to mid-12th centuries AD, carried subtype 3K, which has been recorded at 7th–13th century AD sites in Turkey, Hungary and Denmark, but not previously in Britain. We suggest that travellers to the Holy

Land might have been responsible for the transmission of subtype 3K from southeast Europe to Britain.

Khan, S., Fu, P., 2020. Biotechnological perspectives on algae: a viable option for next generation biofuels. Current Opinion in Biotechnology 62, 146-152.


Because of their biofuel producing capabilities, algae (including microalgae and cyanobacteria) are effective and sustainable tools to attain energy security with a growing world population and for reduction of our current reliance on fossil fuels. Algal metabolic and genetic engineering could provide substantial advancements in producing novel and promising strains for the production of alternative biofuels. In this review, we have highlighted biotechnological strategies for microalgae and cyanobacteria that target the improvement of: (1) biosynthesis of biofuel precursors (fatty acid, TAGs, and lipids etc.), (2) carbon-capture ability to accumulate more lipids, and (3) engineering hydrogenases for augmented production of biohydrogen. Other strategies for improving quality and quantity of algal biofuels are also explored.

Khomarbaghi, Z., Shavandi, M., Amoozegar, M.A., Dastgheib, S.M.M., 2019. Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study. International Journal of Environmental Science and Technology 16, 7849-7860.

https://doi.org/10.1007/s13762-018-02198-y

Studding the diversity of soil indigenous microorganisms, and monitoring effect of contaminants on microbial population, is very critical for understanding microbial activity during bioremediation and selecting successful remediation strategy. To simulate the natural environment, four microcosms were prepared by artificially contaminating clean soil with defined amounts of petroleum hydrocarbons including alkanes mixture (C13–C20), polyaromatic hydrocarbons (PAHs) mixture (anthracene, phenanthrene, fluoranthene, pyrene and benzo (α) pyrene) and both alkanes and PAHs. Contaminants degradation and heterotrophic bacterial count were measured during a 6-month study. Copy number of alkB and C23DO genes was studied using real-time PCR, and bacterial diversity was monitored by 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE). Results indicated that all types of contaminants (except the five ring benzo (α) pyrene) were totally degraded after 6 months and the increase in hydrocarbon degradation rate coincided with the enhancement of total heterotrophic bacterial count in each microcosm. Real-time PCR results showed a significant increase in the copy number of both alkB and C23DO genes in alkane- and PAHs-contaminated microcosm comparing with the control microcosm, indicating selection for special hydrocarbon degraders in hydrocarbon-amended microcosms. The results of DGGE revealed that the type of contaminant in the same soil has a remarkable influence on soil bacterial community structure. Sequencing of DGGE bands suggested that most of the dominant members of the microbial community of contaminated soil are unculturable bacteria from Proteobacteria and the genus Bacillus.

Kida, M., Jin, Y., Yoneda, J., Oshima, M., Kato, A., Konno, Y., Nagao, J., Tenma, N., 2019. Crystallographic and geochemical properties of natural gas hydrates accumulated in the National Gas Hydrate

Program Expedition 02 drilling sites in the Krishna-Godavari Basin off India. Marine and Petroleum Geology 108, 471-481.


This study presents the crystallographic and geochemical properties of different types of pore-space natural gas hydrate recovered by pressure core operations during the National Gas Hydrate Program (NGHP) Expedition 02 at three study areas in the Krishna-Godavari Basin off eastern India. The gas hydrate is structure I with hydration number n = 6.1–6.2, formed predominantly from microbial methane and small amounts of heavier hydrocarbons up to C3. Hydrate crystal lattice constants are nearly uniform regardless of sediment pore-space size. Ethane concentration varies with clay content and to some extent depth, and its measurement helps resolve the contributions of gases dissolved in pore water to hydrate formation. We also assess the disturbance of the core through drilling, using diffraction techniques and visual observation of hydrate-bearing sediments.

Kida, M., Kondo, M., Tomotsune, M., Kinjo, K., Ohtsuka, T., Fujitake, N., 2019. Molecular composition and decomposition stages of organic matter in a mangrove mineral soil with time. Estuarine, Coastal and Shelf Science 231, 106478.


The molecular composition of soil organic matter (SOM) is important in understanding the elemental cycling of mangrove forests. The aim of the study was to investigate the SOM compositional changes with time in a mangrove mineral soil, which is rarely reported in the literature. A 1-m soil core was collected in the subtropical Fukido River mangrove forest (Okinawa, Japan) and separated into 25-cm sections. Humic acids (HA) and fulvic acids (FA) were extracted from the soil, and their relative abundance and chemical characteristics were analyzed by elemental analysis, stable carbon analysis, spectrophotometric measurement, liquid-state 13C nuclear magnetic resonance spectroscopy, and radiocarbon dating. HA exhibited a clear depth trend in the chemical characteristics, with lower H/C and N/C ratios, higher aromaticity, and higher phenolic 13C NMR peaks in the deeper sections. FA did not show such a clear depth trend, and was enriched in O-containing functional groups. A combination of radiocarbon dating and structural analysis of HA indicated that the rapid structural changes in HA (H/C and N/C) occurred during the first years–decades, followed by a gradual change over a time scale of several hundred (~500) years, and these structural changes were best explained by an increase in the relative phenolic C contents. These results show that mangrove SOM is a complex mixture of organic fractions with different biogeochemical reactivities.

Killingsworth, B.A., Sansjofre, P., Philippot, P., Cartigny, P., Thomazo, C., Lalonde, S.V., 2019. Constraining the rise of oxygen with oxygen isotopes. Nature Communications 10, 4924.

https://doi.org/10.1038/s41467-019-12883-2

After permanent atmospheric oxygenation, anomalous sulfur isotope compositions were lost from sedimentary rocks, demonstrating that atmospheric chemistry ceded its control of Earth’s surficial sulfur cycle to weathering. However, mixed signals of anoxia and oxygenation in the sulfur isotope record between 2.5 to 2.3 billion years (Ga) ago require independent clarification, for example via oxygen isotopes in sulfate. Here we show <2.31 Ga sedimentary barium sulfates (barites) from the

Turee Creek Basin, W. Australia with positive sulfur isotope anomalies of ∆33S up to + 1.55‰ and low δ18O down to −19.5‰. The unequivocal origin of this combination of signals is sulfide oxidation in meteoric water. Geochemical and sedimentary evidence suggests that these S-isotope anomalies were transferred from the paleo-continent under an oxygenated atmosphere. Our findings indicate that incipient oxidative continental weathering, ca. 2.8–2.5 Ga or earlier, may be diagnosed with such a combination of low δ18O and high ∆33S in sulfates.

Kim, J., Chhetri, G., Kim, I., Kim, H., Kim, M.K., Seo, T., 2019. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. Journal of Microbiology 57, 959-966.

https://doi.org/10.1007/s12275-019-9007-9

A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7–90.4% and 22–39.6%, respectively. The major fatty acids of strain 17Sr1-28T were summed feature 8 (C18:1ω7c and/or C18:1ω6c), and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is proposed.

Kim, J., Dai, S., Jang, J., Waite, W.F., Collett, T.S., Kumar, P., 2019. Compressibility and particle crushing of Krishna-Godavari Basin sediments from offshore India: Implications for gas production from deep-water gas hydrate deposits. Marine and Petroleum Geology 108, 697-704.


Depressurizing a gas hydrate reservoir to extract methane induces high effective stresses that act to compress the reservoir. Predicting whether a gas hydrate reservoir is viable as an energy resource requires enhanced understanding of the reservoir's compressibility and susceptibility to particle crushing in response to elevated effective stress because of their impact on the long-term permeability and geomechanical stability of the reservoir. This study investigates physical and geomechanical properties of natural sediments with and without tetrahydrofuran (THF) hydrate subjected to high effective stresses of up to 25 MPa. Experimental results show the stiffness of hydrate-free sediments is mainly governed by the stress state and history, while the stiffness of hydrate-bearing sediments reflects both the grain supporting nature of the interconnected hydrate phase and stress effects. The Poisson's ratio of hydrate-bearing sediments at low stresses is

dominated by the Poisson's ratio of the interconnected pore-filling phases, and dominated at high stresses by elastic properties of both the skeleton and pore-filling phases. The stress-void ratio responses of hydrate-bearing sediments above the pre-consolidation stress yields a slightly convex-downward trend, suggesting compressibility is influenced by the stiffness of THF hydrate and sediment grains rather than only by void space reduction. The shape of the compression index (Cc) trend may be attributed to an increasing effective gas hydrate saturation as the total pore volume decreases under loading. The results also show that the presence of THF hydrate in sediments can mitigate particle crushing by suppressing particle rearrangement and supporting a portion of the load that would otherwise have to be carried by the sediment. Therefore, the loss of hydrate crystals during gas production may exacerbate sand crushing.

King, A.J., Bates, H.C., Krietsch, D., Busemann, H., Clay, P.L., Schofield, P.F., Russell, S.S., 2019. The Yamato-type (CY) carbonaceous chondrite group: Analogues for the surface of asteroid Ryugu? Geochemistry 79, 125531.


We report new mineralogical, petrographic and noble gas analyses of the carbonaceous chondrite meteorites Y-82162 (C1/2ung), Y-980115 (CI1), Y-86029 (CI1), Y-86720 (C2ung), Y-86789 (C2ung), and B-7904 (C2ung). Combining our results with literature data we show that these meteorites experienced varying degrees of aqueous alteration followed by short-lived thermal metamorphism at temperatures of >500 °C. These meteorites have similar mineralogy, textures and chemical characteristics suggesting that they are genetically related, and we strongly support the conclusion of Ikeda (1992) that they form a distinct group, the CYs (“Yamato-type”). The CY chondrites have the heaviest oxygen isotopic compositions (δ17O ˜12‰, δ18O ˜22‰) of any meteorite group, high abundances of Fe-sulphides (˜10 ‒ 30 vol%) and phosphates, and contain large grains of periclase and unusual objects of secondary minerals not reported in other carbonaceous chondrites. These features cannot be attributed to parent body processes alone, and indicate that the CYs had a different starting mineralogy and/or alteration history to other chondrite groups, perhaps because they formed in a different region of the protoplanetary disk. The short cosmic-ray exposure ages (≤1.3 Ma) of the CY chondrites suggest that they are derived from a near-Earth source, with recent observations by the Hayabusa2 spacecraft highlighting a possible link to the rubble-pile asteroid Ryugu.

Kinoshita, M., Ijiri, A., Haraguchi, S., Jiménez-Espejo, F.J., Komai, N., Suga, H., Sugihara, T., Tanikawa, W., Hirose, T., Hamada, Y., Gupta, L.P., Ahagon, N., Masaki, Y., Abe, N., Wu, H.Y., Nomura, S., Lin, W., Yamamoto, Y., Yamada, Y., 2019. Constraints on the fluid supply rate into and through gas hydrate reservoir systems as inferred from pore-water chloride and in situ temperature profiles, Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 368-376.


We estimate the rate of upward pore fluid flow and chlorinity (Cl−) concentrations at depth through a joint analysis of Cl− concentration and temperature versus depth profiles obtained from gas hydrate related test sites drilled and cored in the Krishna-Godavari Basin off the eastern coast of India. Cl−, measured on conventional core samples, decreases with depth at all sites but some of the Cl−profiles show a prominent convex shape, whereas in situ temperature profiles, obtained by the

Advanced Piston Coring Temperature probe, are mostly linear at all sites established during the National Gas Hydrate Program 02 Expedition (NGHP-02).

Assuming a one-dimensional, time-dependent model for the advection of pore fluid including the sedimentation effect and depth-dependent diffusivity, we estimate darcy velocity and the Cl− concentrations at depth. The best-fit darcy velocity of 1.2–1.6 × 10−11 m/s was estimated for the sites along the crest of the regional anticlinal structure in the NGHP-02 Area B, which was significantly faster than those on the flanks of the anticline. Because the thermal diffusion coefficient is much larger than the chloride ion diffusion coefficient, estimated darcy velocities are not great enough to generate nonlinear temperature profiles with depth, which is consistent with observed linear thermal profiles.

Kirpes, R.M., Bonanno, D., May, N.W., Fraund, M., Barget, A.J., Moffet, R.C., Ault, A.P., Pratt, K.A., 2019. Wintertime Arctic sea spray aerosol composition controlled by sea ice lead microbiology. ACS Central Science 5, 1760-1767.

https://doi.org/10.1021/acscentsci.9b00541

The Arctic is experiencing the greatest warming on Earth, as most evident by rapid sea ice loss. Delayed sea ice freeze-up in the Alaskan Arctic is decreasing wintertime sea ice extent and changing marine biological activity. However, the impacts of newly open water on wintertime sea spray aerosol (SSA) production and atmospheric composition are unknown. Herein, we identify SSA, produced locally from open sea ice fractures (leads), as the dominant aerosol source in the coastal Alaskan Arctic during winter, highlighting the year-round nature of Arctic SSA emissions. Nearly all of the individual SSA featured thick organic coatings, consisting of marine saccharides, amino acids, fatty acids, and divalent cations, consistent with exopolymeric secretions produced as cryoprotectants by sea ice algae and bacteria. In contrast, local summertime SSA lacked these organic carbon coatings, or featured thin coatings, with only open water nearby. The individual SSA composition was not consistent with frost flowers or surface snow above sea ice, suggesting that neither hypothesized frost flower aerosolization nor blowing snow sublimation resulted in the observed SSA. These results further demonstrate the need for inclusion of lead-based SSA production in modeling of Arctic atmospheric composition. The identified connections between changing sea ice, microbiology, and SSA point to the significance of sea ice lead biogeochemistry in altering Arctic atmospheric composition, clouds, and climate feedbacks during winter.

Kivell, T.L., 2019. Fossil ape hints at how walking on two feet evolved. Nature 575, 445-466.

https://www.nature.com/articles/d41586-019-03347-0

Approximately 11.6-million-year-old fossils reveal an ape with arms suited to hanging in trees but human-like legs, suggesting a form of locomotion that might push back the timeline for when walking on two feet evolved.

Ever since Charles Darwin’s work provided the basis for understanding human evolution, there have been long-standing questions regarding when, why and how our early human ancestors begin to walk on two feet. The commitment to terrestrial bipedalism, characterized by skeletal adaptations for walking regularly on two feet, is a defining feature that enables the assignment of fossils to the hominin lineage — which comprises all species more closely related to humans than to chimpanzees

(Pan troglodytes) or bonobos (Pan paniscus), our two closest living relatives. On the basis of fossil findings, some of which are more controversial than others1,2, the answer to the ‘when’ question is thought to be between 7 million and 5 million years ago at the end of the Miocene epoch (which lasted from about 23 million to 5 million years ago).

Answering the questions of why and how hominin bipedalism evolved depends a lot on what kind of locomotion was being used before terrestrial bipedalism evolved. Did it evolve from an ancestor that lived mainly in trees, or were these ancestors already walking on all fours on the ground and subsequently evolved to stand up and walk on two feet? Writing in Nature, Böhme et al.3 report the discovery of an ape species called Danuvius guggenmosi from the middle of the Miocene. This species moved around in a previously unknown way, which the authors suggest could provide a model for the type of locomotion from which hominin bipedalism evolved.

Questions about the origin of hominin bipedalism and how the last common ancestor of humans, chimpanzees and bonobos might have moved are conventionally addressed using either a top-down or a bottom-up approach (Fig. 1). Darwin4 and many palaeoanthropologists favoured the top-down approach, examining living primates, particularly the great apes, for clues to how bipedalism evolved5,6. African apes — chimpanzees, bonobos and gorillas (of the genus Gorilla) — go into the trees to eat, sleep and when they need protection, but spend most of their time on the ground, using their knuckles for walking. Given our close genetic relationship to these apes, and because we also share certain features of our hands and feet with them, some have argued that hominin bipedalism evolved from a knuckle-walking ancestor5, or a more generalized quadruped lacking knuckle-walking specializations7, that divided its time between the ground and the trees. By contrast, others have noted that the way that orangutans (of the genus Pongo) move bipedally in trees, and the mechanical similarities between how apes use their legs for climbing and how humans use theirs for walking, suggest that bipedalism evolved from an ape ancestor that was previously committed to life in the trees6,8.

Although logical, this top-down approach is constrained, as Darwin acknowledged4, to examining evidence from the few remaining living ape species. However, one of the earliest potential hominins for which we have the most fossil evidence — the approximately 4.4-million-year-old Ardipithecus ramidus — is argued to be distinctly unlike living great apes in its anatomy, which suggests that the African apes and Asian orangutans we know today are actually quite specialized in their locomotor behaviours compared with their earlier ancestors7. Each living ape species is a result of its own long, evolutionary history, and, in the case of African apes, one that we often forget because there is so little fossil evidence of it. This absence of fossil information to reveal how African apes evolved makes questions about the nature of our common ancestor even trickier to answer.

Other palaeoanthropologists address the question of bipedal origins from a bottom-up approach instead, looking to the approximately 30 genera of fossil apes that have been identified from the Miocene of Africa, Asia and Europe as potential models for what our last common ancestor might have looked like2,7,9. However, these apes show a hotchpotch of skeletal adaptations, with features found in combinations that are unlike anything we see in living primates, and that often leave us guessing about how these animals moved around and how much time they spent in trees or on the ground.

The teeth of D. guggenmosi identify it as belonging to a group of fossil ape species called dryopithecins that have been found from the mid- to late Miocene in Europe and that some consider to be ancestral to African apes9. Living African ape species inhabit the equatorial region of

Africa, but, during certain times of the Miocene, many ancestral great apes were living throughout Europe and Asia and migrating both to and out of Africa. Some researchers suggest that the dryopithecins show features found in chimps and gorillas today and therefore make good candidates for the ancestors of living African apes9. The D. guggenmosi skeleton is unique compared with other dryopithecin specimens, both in its preservation of two, almost complete, limb bones — an ulna (a forearm bone) and a tibia (a leg bone) — and in the combination of characteristics it displays. Böhme et al. focus their attention on a baboon-sized and probably male partial skeleton. As well as the ulna and tibia, the skeleton includes some vertebrae, a partial thigh bone (femur), and hand and foot bones.

The length of the ulna relative to the tibia shows that the forearm of D. guggenmosi was long relative to the leg, similar to a bonobo’s form. Combined with a flexible elbow and hand bones indicating a powerful, grasping thumb and curved fingers, the forelimb has the telltale signs of arboreal suspension found in all living great apes.

However, the lower limb of D. guggenmosi tells a different story, and one that is more reminiscent of human lower limbs than of those of other great apes. The shape of the joints of the femur and tibia suggests the use of extended (upright) hip and knee postures that differ from the bent hips and knees that living African apes use when they occasionally walk bipedally on the ground or in trees. The top of the tibia is reinforced, and the ankle joint is stable, properties that are adaptations for resisting the higher load placed on the lower leg when moving on two limbs instead of four. But the foot has a long, robust big toe that would be good for grasping, suggesting that D. guggenmosi might have walked flat-footed on branches (Fig. 2). Whether or not it regularly walked bipedally on the ground is less clear.

Together, the mosaic features of D. guggenmosi arguably provide the best model yet of what a common ancestor of humans and African apes might have looked like. It offers something for everyone: the forelimbs suited to life in the trees that all living apes, including humans, still have; lower limbs suited to extended postures like those used by orangutans during bipedalism in the trees8; and further specialization of such features of the lower limbs in humans to enable habitual terrestrial bipedalism.

If it is accepted that the locomotor behaviours observed in living great apes and humans evolved from an ancestor that used extended limb clambering, this would answer the question of what kind of early locomotion underlies our bipedal origins. And that would get us closer to answering why and how our human ancestors became less dependent on life in the trees and fully embraced two-footed terrestrial locomotion. Until more fossil evidence of how African apes evolved is found, a bottom-up approach from the Miocene is probably our best means of deciphering the evolution of one of our most defining human features.

References

1. Wood. B. & Harrison, T. Nature 470, 347–352 (2011).

2. Almécija, S. et al. Nature Commun. 4, 2888 (2013).

3. Böhme, M. et al. Nature 575, 489–493 (2019).

4. Darwin, C. The Descent of Man (Murray, 1871).

5. Richmond, B. G., Begun, D. R. & Strait, D. S. Am. J. Phys. Anthropol. 116, 70–105 (2001).

6. Crompton, R. H., Seller, W. I. & Thorpe, S. K. S. Phil. Trans. R. Soc. B 265, 3301–3314 (2010).

7. Lovejoy, C. O. Science 326, 74 (2009).

8. Thorpe, S. K. S., Holder, R. L. & Crompton, R. H. Science 316, 1328–1331 (2007).

9. Begun, D. R., Nargolwalla, M. C. & Kordos, L. Evol. Anthropol. 21, 10–23 (2012).

10. Ward, C. V. in Handbook of Paleoanthropology (eds Henke, W. & Tattersall, I.) 1363–1386 (Springer, 2015).

11. Morgan, M. E. et al. Proc. Natl Acad. Sci. USA 112, 82–87 (2015).

Klewiah, I., Berawala, D.S., Alexander Walker, H.C., Andersen, P.Ø., Nadeau, P.H., 2020. Review of experimental sorption studies of CO2 and CH4 in shales. Journal of Natural Gas Science and Engineering 73, 103045.


In recent years CO2 injection in shale has been investigated with aim to enhance shale gas recovery (ESGR) and permanently sequester CO2. This paper reviews the state of research on CH4 and CO2 sorption in shale. We present the interaction of CO2 and CH4 with shale rocks and discuss the dependence of gas sorption on shale properties including organic matter content, kerogen type, mineralogy, moisture and temperature as well as shale selectivity for either species. Dynamic CO2-CH4 exchange studies are also summarized together with the geochemical and mechanical impact of gas sorption in shales. We note that most experimental work is still performed on crushed samples rather than whole cores. Also, CO2 is preferentially adsorbed over CH4 when both species co-exist in shale. Both gases are in supercritical state at typical reservoir conditions. Especially CO2 adsorption is not well described by standard isotherm models in this state.

Klun, K., Falnoga, I., Mazej, D., Šket, P., Faganeli, J., 2019. Colloidal organic matter and metal(loid)s in coastal waters (Gulf of Trieste, northern Adriatic Sea). Aquatic Geochemistry 25, 179-194.

https://doi.org/10.1007/s10498-019-09359-6

Large volumes of seawater were sampled in the Gulf of Trieste (northern Adriatic Sea) in order to study the interactions between colloidal organic matter (COM) and metal(loid)s (Me) in coastal waters. COM (> 5 kDa) was isolated by ultrafiltration and characterized using 1H NMR spectroscopy and elemental Corg. and Ntot. analyses. COM in the gulf represents about one quarter of the dissolved organic carbon (DOC), and according to 1H NMR analysis, it is composed of polysaccharides (30–45%), lipids (30–55%), proteins and carboxyl-rich alicyclic molecules (CRAM) (15–20%), and humics (< 1%). An accumulation of COM was observed in the late spring–early summer. The polysaccharide and lipid fractions increased up to twofold and the protein fraction decreased, reflected in a higher Corg./Ntot. (28, molar) ratio. Higher concentrations of humics were observed due to local freshwater discharges in spring. COM from the Isonzo/Soča River differed from the marine COM exhibiting higher protein/CRAM and higher humic contents. COM from the Isonzo/Soča mouth at salinities 16–33 was compositionally similar to marine COM. Analysis of Me, performed by ICP-MS and CVAFS

(Hg), showed that Hg (nearly 100%), Cu (20%), Cr (10%), and Se (10%) have the highest Me affinity to colloids. Similar to COM, Hg and Cu rapidly increased till summer due to their sequestration in accumulated COM (transfer to particulate phase). The observed Me/Corg. ratios (Co, Cd, Hg < U, Cr, Ni, Mn < As, Zn, Cu, V < Se, Al, Fe) differ somewhat from those of the Irving–Williams series and can be explained by the composition of COM and variable background concentrations of studied Me in the northern Adriatic. Data from the salinity gradient in the metal-contaminated (especially Hg, Pb, Zn) Isonzo/Soča mouth showed flocculation of Al and Ba and desorption of V, Co, As, Se, Cs, U, and Hg, from the riverine particles with increasing ionic strength, while Fe, Mn, Cu, Cr, Ni, Zn, Cd, and Pb did not correlate with salinity.



The Atacama Desert frequently serves as model system for tracing life under extremely dry conditions. We hypothesized that traces of life in the Atacama Desert follow distinct micro- and macro-scale gradients such as soil depth and elevation, respectively. Different depth intervals of surface soils (0–1, 1–5, and 5–10 cm) were sampled at five sites along an elevational transect near the Quebrada Aroma, spanning from the hyperarid core of the desert towards the arid Western Andean Precordillera (1300 to 2700 m a.s.l.), and from one additional site in the hyperarid core near Yungay. We determined the contents of major elements, pedogenic minerals and oxides, organic carbon (OC), and its δ13C and δ15N isotopic composition. The presence of living microorganisms was assessed by cultivation, and bacterial community composition was analyzed based on 16S rRNA gene sequencing. Additional information about past and present plant and microbial life was obtained from lipid biomarker analysis. We did not detect consistent micro-scale distributions for most of these proxies within the soils. However, concentrations of OC and of long-chain, plant wax-derived n-alkanes increased in soils along the aridity gradient towards the wetter sites, indicating the presence of past life at places presently not covered by vegetation. Likewise, bacterial abundance and diversity decreased as hyperaridity increased and the microbial community composition changed along the transect, becoming enriched in Actinobacteria. The distributional patterns of phospholipid fatty acids (PLFAs) confirmed the larger bacterial diversity at the higher, more humid sites compared to the drier ones. Archaeal isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) and bacterial branched (br)GDGTs, which can also indicate past life, did not follow a clear elevational trend and were absent at the driest site. Taken together, plant-derived and microbiological markers follow primarily the macro-scaled elevation and aridity gradient. Viable bacteria are present even at the driest sites, while detected biomolecules also indicate past life. The detection of past plant life in nowadays apparently lifeless regions suggests that conditions for life were less hostile in former times.

Kölling, M., Bouimetarhan, I., Bowles, M.W., Felis, T., Goldhammer, T., Hinrichs, K.-U., Schulz, M., Zabel, M., 2019. Consistent CO2 release by pyrite oxidation on continental shelves prior to glacial terminations. Nature Geoscience 12, 929-934.

https://doi.org/10.1038/s41561-019-0465-9

Previous evidence suggests enhanced pyrite oxidation on exposed continental shelves during glacial phases of low sea level. While pyrite oxidation directly consumes atmospheric oxygen, acid generated by this reaction should increase the release of CO2 through carbonate dissolution. This scenario represents a climate control loop that could temper or even prevent glacials because increasing CO2 triggers warming and rising sea level. However, the amplitudes of sea-level changes increased over the Quaternary, and CO2 concentrations co-varied with sea level throughout most of the past 800,000 years. Only during peak glacial conditions did CO2 levels reach an apparent lower threshold independent of falling sea level. Here we suggest that during the last nine glacial–interglacial cycles, pyrite-oxidation-driven release of CO2 and consumption of O2 occurred during 10 kyr to 40 kyr periods preceding glacial terminations. We demonstrate that repeated sea-level lowstands force pyrite oxidation to ever-greater depths in exposed shelf sediments and cause CO2 release that could explain the glacial CO2 threshold. When the duration of interglacials with high sea level is insufficient to restock the shelf pyrite inventory, this CO2-releasing process represents a discharging ‘acid capacitor’.

Kong, X., Jiang, Z., Han, C., Zhang, R., 2020. Organic matter enrichment and hydrocarbon accumulation models of the marlstone in the Shulu Sag, Bohai Bay Basin, Northern China. International Journal of Coal Geology 217, 103350.


Hybrid unconventional systems are composed of juxtaposed organic-rich and organic-lean intervals. Organic matter enrichment, hydrocarbon migration, and the spatial relationship of source rocks and reservoirs have important influences on differential hydrocarbon accumulation within the system. Most studies have ignored the complexity of hydrocarbon accumulation in unconventional oil reservoirs. A typical hybrid lithology system with a combination of marlstone and rudstone has been discovered in the lower part of the third member of the Shahejie Formation of the Shulu Sag, Bohai Bay Basin, Northern China. The basin showcases a strong heterogeneity in unconventional hydrocarbon production and is an appropriate case to study hydrocarbon accumulation within hybrid unconventional systems. However, relevant work in the study area was scarce. A study of the mechanisms of organic matter enrichment and hydrocarbon accumulation was required to understand the heterogeneity of the oil reservoirs. Nine units in ascending order, namely IL, IU, IIL, IIU, IIIL, IIIU, IV, VL, and VU, were proposed in this study. A detailed geochemical analysis was carried out to distinguish the organic matter sources and preservation conditions among the different units, and assess the migration patterns of the hydrocarbons. The results show that Unit IIL has the highest total organic carbon (TOC) content. Unit IIL has a higher quantity of aquatic sourced organic matter, with relatively high abundance of short chain n-alkanes, C27/C29 sterane, and 4-methyl steranes. Based on the low ratios of pristane to phytane, the varve-like lamination structure of the lithology and suitable salinity, we can speculate that good organic matter preservation conditions existed in Unit IIL. Maturity of the source rocks increases with depth. Biomarkers indicate that hydrocarbons within the marlstones were retained in situ, whereas hydrocarbons within the rudstones were derived from source rocks via short- or long-distance migrations. Fractures can act as effective pathways for hydrocarbon migration. Organic matter sources, preservation conditions, maturity, and hydrocarbon migration ways jointly controlled the formation of oil reservoirs in the Shulu Sag. The results of this study provide a better understanding of organic matter enrichment and hydrocarbon accumulation and guide further exploration in the basin.

Konno, Y., Kato, A., Yoneda, J., Oshima, M., Kida, M., Jin, Y., Nagao, J., Tenma, N., 2019. Numerical analysis of gas production potential from a gas-hydrate reservoir at Site NGHP-02-16, the Krishna–Godavari Basin, offshore India–Feasibility of depressurization method for ultra-deepwater environment. Marine and Petroleum Geology 108, 731-740.


Sandy gas-hydrate reservoirs are considered to be promising deposits for gas recovery, but the feasibility of the depressurization method in ultra-deepwater environments remains unclear because high pressure gradient induced by depressurization may increase the water production and reduce the gas–water ratio of produced fluid. In numerical simulations, this study predicts the gas production behavior of a hydrate reservoir (Site NGHP-02-16 in the Krishna–Godavari Basin, offshore India) located in ultra-deepwater (depth 2546.5 m). The reservoir properties such as the hydrate saturation and initial effective (in-situ) permeability were determined from log data and pressure-core analysis. By comparing the hydrate saturations calculated from resistivity log with the estimations from P-wave velocities of pressure-cores, the model parameters a, m, and n of Archie's equation were determined as 1.8, 2.0, and 2.9, respectively. The initial effective permeability of the hydrate-bearing layers (with up to 78% hydrate saturation) was estimated to range from approximately 0.01 to 1.0 millidarcy (mD). At day 180 after the start of depressurization in a single vertical well, the gas production rates ranged from 320 to 9500 Sm3/d, depending on the bottom-hole pressure. Lowering the bottom-hole pressure increased the gas production rate and gas–water ratio of the produced fluid. The bottom-hole pressure of 10 MPa or less is recommended for the production test condition in this site; however, aquifer below the gas-hydrate-bearing zone and poor hydraulic sealing of the over- and under-burden increased the water production. Hydraulic isolation of the gas-hydrate-bearing layers is essential when applying depressurization in an ultra-deepwater environment.

Korasidis, V.A., Wagstaff, B.E., 2020. The rise of flowering plants in the high southern latitudes of Australia. Review of Palaeobotany and Palynology 272, 104126.


The Early Cretaceous high-paleolatitude palynofloras from the Otway and Gippsland basins of southeastern Australia contain diverse angiosperm assemblages not described previously. Clavatipollenites hughesii recovered from the early Aptian Upper Cyclosporites hughesii subzone in the Gippsland Basin represents the first record of angiosperm pollen in Australia, coeval to records recovered from the Great Artesian and North West Shelf basins of northern Australia. Tricolpate pollen including Tricolpites variabilis, Rousea georgensis and Striatopollis spp., are first recorded in the late Albian Upper Coptospora paradoxa subzone in southeastern Australia. This represents the second oldest occurrence of tricolpate pollen in Australia, the first occurring in the older middle Albian Lower Coptospora paradoxa subzone in the northern Great Artesian Basin. By the latest Albian Phimopollenites pannosus Zone angiosperms had diversified rapidly in southeastern Australia. The delayed appearance, rise in abundance and diversification of eudicot angiosperms in the high-latitude southern basins of Australia, relative to low- and mid-latitude settings, supports a latitudinally diachronous pattern of angiosperm range expansion from warmer paleoequatorial regions to relatively cooler high-latitude settings. Increasing mean annual temperatures globally in the late Albian likely facilitated the expansion of angiosperms into high-latitude settings in the Southern and Northern hemispheres.

Kot, D., Macko, T., Arndt, J.-H., Brüll, R., 2019. Porous graphite as platform for the separation and characterization of synthetic polymers – an overview. Journal of Chromatography A 1606, 360038.


Porous graphite as sorbent differs significantly from all other HPLC column packings. It stands out due to its chemically extremely homogeneous surface, which moreover is planar on an atomic level. This sorbent, according to its non-polar but polarizable surface, is able to adsorb polar as well as non-polar small molecules as well as macromolecules. Moreover, it enables their separation induced by minute differences in their molecular architecture, which includes the aspects of planarity, branching or tacticity of macromolecules. Although graphite had already been used many years for the separation of small molecules, the application of porous graphite for separations in the domain of synthetic polymers has been rare. In 2009 it was found that porous graphite enables the separation of polyethylene and polypropylene on the basis of their full adsorption and desorption, when suitable solvents are used. This approach has led to the fast elaboration of HPLC systems for separations of various polar modified as well as non-polar polyolefins. Due to pronounced adsorptive interactions, porous graphite is applicable even at temperatures as high as 160 °C. The results presented in this paper manifest that porous graphite enables to obtain important information about the composition distribution of various synthetic polymers, the architecture of macromolecules (i.e., branching) or their tacticity, and underlines its enormous application potential.

Kradra Brahma, K., Bendedouch, D., Bouhadda, Y., Bouanani, F., Bounaceur, B., Sardi, A., 2019. Stability of Hassi-Messaoud asphaltenes in media of different polarities. Petroleum Chemistry 59, 1190-1194.

https://doi.org/10.1134/S0965544119110094

The aim of this work is to explore the floculation behavior of asphaltenes (extracted from a deposit recovered from a Hassi-Messaoud oil well) in solution in toluene according to the polarity of the flocculating medium. The flocculation thresholds related to the addition of two flocculating agents of different polarities (n-heptane and acetone) for three asphaltenic concentrations are obtained by means of near infra-red absorption spectrophotometry. The Hildebrand solubility parameters of the flocculated asphaltenic fractions are deduced using the Donnagio method based on the Flory−Huggins theory. The results obtained indicate that the interactions between the flocculated asphaltenic molecules within the toluene/acetone mixture are weaker than those in the toluene/n-heptane mixture.

Kuang, H.-w., Fan, Z.-x., Liu, Y.-q., Peng, N., Zhu, Z.-c., Yang, Z.-r., Wang, Z.-x., Yu, H.-l., Zhong, Q., 2019. Stromatolite characteristics of Mesoproterozoic Shennongjia Group in the northern margin of Yangtze Block, China. China Geology 2, 364-381.


ABSTRACT Mesoproterozoic Shennongjia Group in Shennongjia Area can be divided into three subgroups in ascender order. Of which the lower subgroup includes Yingwodong, Dayanping, Macaoyuan, Luanshigou, Dawokeng and Kuangshishan formations; the middle subgroup is formed

by Yemahe, Wenshuihe and Shicaohe formations; the upper subgroup consists of Songziyuan and Wagangxi formations. Stromatolites developed very well in the carbonate rocks of each subgroup in Shennongjia Group. Based on descriptions of stromatolites macrotypes and their characteristics, this paper studied the formation environments, discussed the relationship among types, sizes, abundance of stromatolites and sedimentary environment, and established the formation and development pattern of stromatolites. As a result, this research also reveals the paleoenvironment and paleoclimate during the period of the Shennongjia Group deposited, which is beneficial to the study of paleoenvironment, paleogeography and paleoclimate, stratigraphic succession and regional correlation of the northern edge of Yangtze block. Stromatolites of Shennongjia Group are mainly conical, columnar, domal, wavy, stratiform and stromatolite reefs. The columnar and conical stromatolites are well developed. Conical stromatolites are mainly monomers, with a variety of pyramidal types, ranging in diameter from a few millimeters to several meters and formed in the high energy subtidal zone and tidal lagoon environment. Most of the columnar stromatolites are medium to small sizes implied a wide and gentle slope environment at that time. Stratiform (including wavy) stromatolites are larger scales and extends far away and distributed most widely in almost every horizon in the carbonate rocks. Stratiform stromatolites can be formed in low energy environments such as subtidal and intertidal zones and supratidal belts. Wavy stromatolites often developed in the hydrodynamic energy condition from weak energy intertidal zone gradually strengthened to the below of the high energy supratidal. Although stromatolite reefs can be a single or multiform combination, they developed mainly consisted of laminar or small walled columnar and large domal stromatolites. Shicaohe Formation also partially developed large domical stromatolites, the depositional environment is from the upper intertidal to supratidal zone. Stromatolite in Shennongjia Group usually appears as a combination of “Stratiform (wavy)-dome-columnar-coniform” or “stratiform-dome-coniform-columnar-dome-stratiform” vertieally, which represents the seawater depth from shallower to deeper or from shallow to deep and then to shallow again. These phenomenons generally reflected a stable sea level and companied with a high frequency oscillation. Comprehensive researches on the stratigraphy, sedimentary facies, sedimentary environment and the stromatolite types and their characteristics in the Shennongjia Group indicated that the Shennongjia Area is located on a gentle slope of carbonate platform in the passive continental edge, generally, i.e., one of warm and humid climate shallow water zone or/and a cold-drought climate, and had been experienced with eustatic cycles during the Shennongjia Group deposited.

Kumar, P., Collett, T.S., Shukla, K.M., Yadav, U.S., Lall, M.V., Vishwanath, K., 2019. India National Gas Hydrate Program Expedition-02: Operational and technical summary. Marine and Petroleum Geology 108, 3-38.


The India National Gas Hydrate Program is being steered by the government of India's Ministry of Petroleum and Natural Gas (MoPNG) with participation of Directorate General of Hydrocarbons (DGH), Oil and Natural Gas Corporation Limited (ONGC), and the National Oil Companies and Research Institutes of India. The India National Gas Hydrate Program Expedition 01 (NGHP-01) established the presence of gas hydrate in the Krishna Godavari (KG) and Mahanadi Basins and in the offshore area of the Andaman Sea Basin. However, the gas hydrates discovered during NGHP-01 were mainly distributed as fracture-filling material in fine-grained clay-rich sediments. The India National Gas Hydrate Program Expedition 02 (NGHP-02) was carried out with an objective to

discover gas hydrate in sand-rich sediment along the eastern offshore margin of India. ONGC planned and executed NGHP-02 on the behalf of the MoPNG.

NGHP-02 started on March 3, 2015 and was completed on July 28, 2015 (total 147 days) using the Japanese scientific Drilling Vessel Chikyu (D/V Chikyu). During NGHP-02, 42 holes at 25 sites were drilled, cored, and/or surveyed with downhole logging tools. These sites were located in four areas along the eastern margin of India and formally named Area A (Mahanadi Basin, three sites), Area B (northern part of the KG-Basin, twelve sites), Area C (central part of the KG-Basin, six sites), and Area E (southern part to the KG-Basin, four sites). All 25 sites established during NGHP-02 were first drilled and logged with logging-while-drilling (LWD) tools and an additional 17 holes were then drilled and/or cored with conventional coring tools (HPCS/ESCS) or pressure coring tools (PCTB). Wireline logging was conducted in 10 holes and formation tests using a dual packer Modular Formation Dynamics Tester (MDT) tool were carried out in two holes.

The onboard science team used the laboratory facilities on the D/V Chikyu to examine and analyse the physical properties, geochemistry, and sedimentology of all the cores collected during the expedition. Core samples were also analysed in additional post-expedition shore-based studies conducted in numerous domestic and international gas hydrate research laboratories. The NGHP-02 sediment cores were archived at the National Gas Hydrate Core Repository in Mumbai (India), which is associated with the ONGC Gas Hydrate Research and Technology Centre (GHRTC). The necessary data for characterizing the occurrence of gas hydrate, such as interstitial water chlorinities, core-derived gas chemistry, physical and sedimentological properties, thermal images of the recovered cores, pressure core and downhole measured logging data (LWD and/or conventional wireline log data), were obtained from most of the drill sites established during NGHP-02. Almost all the drill sites yielded evidence for the occurrence of gas hydrate; however, the inferred in situ concentration of gas hydrate varied substantially from site to site. For the most part, the interpretation of downhole logging data, core thermal images, interstitial water analyses, and pressure core images from the sites established during NGHP-02 indicate that the occurrence of concentrated gas hydrate is mostly associated with coarser grained (sand-rich) sediments. This paper presents the operational and technical summary of NGHP-02.

Kumar, P., Collett, T.S., Yadav, U.S., Singh, J., 2019. Formation pressure and fluid flow measurements in marine gas hydrate reservoirs, NGHP-02 expedition, offshore India. Marine and Petroleum Geology 108, 609-618.


Open Hole Modular Dynamic Testing (MDT) measurements were conducted in a gas hydrate-bearing sand-rich reservoir offshore India during the National Gas Hydrate Program 02 (NGHP-02) Expedition. The primary goal of this test was to obtain effective reservoir petrophysical properties in the presence of gas hydrates. The test plan included a series of pre-hydrate dissociation flow and build-up (shut-in) tests, and an attempt to dissociate gas hydrate in a sand-rich reservoir by depressurization to collect formation fluid samples and to further characterize in situ gas hydrate stability conditions. Schlumberger's wireline MDT tool was used in a dual-packer configuration to isolate the formation being tested.

This paper presents the results of the open hole MDT measurements that were conducted in Hole NGHP-02-23-C in Krishna-Godavari Basin at a water depth of 2553.5 m. The MDT dual packer test

was conducted in 27 cm (10.63 in) diameter open hole section of the borehole within a 1-m interval isolated between two inflatable packers with the midpoint of the test interval at 2853.0 m below rig floor (mbrf) (271.0 m below sea floor (mbsf)). This was the first gas hydrate MDT test ever conducted in ultradeep water to characterize a gas hydrate reservoir system. Pre-hydrate dissociation testing was performed with a drawdown period (depressurization) of 20 min followed by a build-up (shut-in) of 20 min. The measured formation pressure was 4090.7 psia and the formation fluid (i.e., water) mobility was calculated at 1.98 mD/cP. During the second dissociation phase of the same test a maximum pressure drawdown of 840 psia was achieved; however, falling short of the 1120 psia drawdown required for dissociation. During the dissociation test the flow line pressure stabilized at a flowing pressure of 3250 psia which can be attributed to the relatively high mobility of the free water phase in the hydrate-bearing reservoir. Good quality formation pressure and near well bore mobility data was acquired that yielded a “high confidence” reservoir effective radial permeability-thickness product of 0.2 mD.m (or a horizontal effective permeability of 0.1 mD assuming a reservoir thicknees of 1.8 m) using pressure transient analysis (radial flow regime was achieved) despite unstable borehole conditions and complex operations in these shallow unconsolidated sedimentary sections.

Kumari, S., Paul, D., Stracke, A., 2019. Constraints on Archean crust formation from open system models of Earth evolution. Chemical Geology 530, 119307.


Establishing the mode and rate of formation of the continental crust is crucial for quantifying mass exchange between Earth’s crust and mantle. The limited crustal rock record, particularly of early Archean rocks, has led to a variety of different models of continental growth. Here, we present an open-system model of silicate Earth evolution incorporating the Sm-Nd and Lu-Hf isotope systematics with the aim to constrain crustal growth during the Archean and its effect on the chemical and isotopic evolution of Earth’s crust-mantle system. Our model comprises four reservoirs: the bulk continental crust (CC), depleted upper mantle (UM), lower mantle (LM), and an isolated reservoir (IR) where recycled crust is stored transiently before being mixed with the LM. The changing abundance of isotope species in each reservoir is quantified using a series of first order linear differential equations that are solved numerically using the fourth order Runge–Kutta method at 1 Myr time steps for 4.56 Gyr (the age of the Earth). The model results show that only continuous and exponential crustal growth reproduces the present-day abundances and isotope ratios in the terrestrial reservoirs. Our preferred crustal growth model suggests that the mass of the CC by the end of Hadean (4.0 Ga) and end of Archean (2.5 Ga) was ∼30% and ∼75% of the present-day mass of the CC, respectively. Models proposing formation of most (∼90%) of the present-day CC during the initial 1 Gyr or nearly 50–60% during the last 1 Gyr are least favorable. Significant mass exchange between crust and mantle, that is, both the formation and recycling of crust, started in the Hadean with Sm-Nd and Lu-Hf isotope evolution typical for mafic rocks. Depletion of the UM (in incompatible elements) during the early Archean is mitigated by the input of recycled crust, so that the UM maintained a near-primitive Hf-Nd isotope composition. The LM also retained a near-primitive Hf-Nd isotope composition during the Archean, but for different reasons. In contrast to the UM, the crustal return flux into the LM is transiently stored (∼ 1 Gyr) in an isolated reservoir (IR), which limits the mass flux into and out of the LM. The IR in our model is distinct from other mantle reservoirs and possibly related to stable crustal blocks or, alternatively, to recycled crust in the mantle that remains temporarily isolated, perhaps at the core-mantle boundary (LLSVPs).

La Nasa, J., Modugno, F., Colombini, M.P., Degano, I., 2019. Validation study of selected ion flow tube-mass spectrometry (SIFT-MS) in heritage science: Characterization of natural and synthetic paint varnishes by portable mass spectrometry. Journal of The American Society for Mass Spectrometry 30, 2250-2258.

https://doi.org/10.1007/s13361-019-02305-4

The identification at molecular level of organic materials in heritage objects as paintings requires in most cases the collection of micro-samples followed by micro-destructive analysis. In this study, we explore the possibility to characterize natural and synthetic resins used as paint varnishes by mean of non-invasive analysis of released volatile organic compounds (VOCs) through selected ion flow tube-mass spectrometry (SIFT-MS). SIFT-MS is a portable direct mass spectrometric technique that achieves the analysis of VOCs at trace levels in real time, by controlled ultra-soft chemical ionization using eight different chemical ionization agents. We tested the portable instrumentation on different reference resins used as paint varnishes, both natural (mastic, dammar, and colophony) and synthetic (Paraloid B67, MS2A, Regalrez 1094, and polyvinyl acetate), to evaluate the possibility to acquire qualitative data for the identification of these materials in heritage objects avoiding any sampling. This new analytical approach was validated by comparison with the traditional approach for VOCs analysis based on solid phase micro extraction-gas chromatography/mass spectrometry (SPME-GC/MS) analysis. The results demonstrate the use of SIFT-MS as an in situ non-invasive and non-destructive mass spectrometric technique to identify organic materials, such as paint varnishes.

Landon, E.N.U., Liu, P.-J., Yin, Z.-J., Sun, W.-C., Shang, X.-D., Donoghue, P.C.J., 2019. Cellular preservation of excysting developmental stages of new eukaryotes from the early Ediacaran Weng’an Biota. Palaeoworld 28, 461-468.


The Ediacaran Weng’an Biota provides a unique window on marine diversity during the interval in which the fundamental animal body plans were being established. Here we describe a previously unreported component of the assemblage, millimeter-scale encysted spheres that exhibit a characteristic but simple slit-shaped excystment mechanism (Sporosphaera guizhouensis n. gen. n. sp.), reminiscent of acritarchs. The cysts contain a large inner body or numerous small discrete membrane-bounded bodies. It is possible that the inner bodies represent disaggregated cells of a multicellular body, like an embryo, but there is no evidence to support this interpretation and the occurrence of the excystment structure is not readily compatible with an embryo interpretation. Rather, we interpret the encysted organisms as multicellular stages within the lifecycle of otherwise probably unicellular eukaryotes. The developmental mode exhibited by Sporosphaera, incorporating a resting stage, implies an adaptation to adverse environmental conditions. This parallels the appearance of Large Ornamented Ediacaran Microfossils (LOEMs) which have been interpreted as diapause stages in the embryology of early animals. Sporosphaera is distinct from LOEMs by ornamentation instead of size, which may implicate that not all LOEMs are animal embryos, if any.

Larichev, Y.V., Kovalenko, E.Y., Mart’yanov, O.N., 2019. Effect of nitrogen bases on the structure of primary asphaltene clusters and dynamics of aggregation of heavy oil fractions. Petroleum Chemistry 59, 1195-1200.

https://doi.org/10.1134/S0965544119110100

Using the method of small-angle X-ray scattering (SAXS), the effect of nitrogen-containing compounds on the structure of primary asphaltene clusters and changes in their structure and size characteristics has been studied. It has been shown that the addition of nitrogen bases leads to a partial degradation of the primary aggregates of asphaltenes and the appearance of a larger number of disordered “non-compact” fragments in the solution, thereby altering the dynamics of the entire aggregation process. Nitrogen bases also provoke a change in the type of packing of the primary particles of asphaltenes, facilitating the formation of a looser secondary structure of asphaltene aggregates.

Laut, L., Vilar, A., Belart, P., Clemente, I., Fontana, L., Pereira, E., Ballalai, J., 2020. Organic matter compounds as a tool for trophic state characterization in a hypersaline environment: Araruama Lagoon, Brazil. Journal of South American Earth Sciences 97, 102403.


Araruama Lagoon, located in Rio de Janeiro (SE, Brazil), is considered the largest hypersaline lagoon in the world. Over the last decades, this environment has been influenced by urban growth around its margins, which has consequently led to the discharge of untreated sewage, particularly during the summer season (December–March). Excessive nutrient discharges may lead to the rapid enrichment of organic and inorganic nutrients and consequently, eutrophication. Within this context, organic matter quality and amount evaluations become an essential tool to assess the trophic state of coastal environments. Therefore, the present study aims to characterize the trophic state and define the depositional dynamics based on biopolymer content (carbohydrates, lipids and proteins), total organic carbon, total sulfur and sediment granulometry at the Araruama Lagoon region affected by urban activities (Itajuru Channel and adjacencies). The integration of physio-chemical water and sediment data allowed for the identification of four regions presenting different trophic condition, namely the Itajuru Channel - sandy with high hydrodynamics and undergoing marine influence; a region influenced by salt-production activity; the innermost region, presenting high protein concentrations originating from microbiological activity and the most eutrophic area, located in a marina activity region, marked by high anthropogenic organic matter levels.

Lavado, N., de la Concepción, J.G., Babiano, R., Cintas, P., Light, M.E., 2019. Interactions of amino acids and aminoxazole derivatives: Cocrystal formation and prebiotic implications enabled by computational analysis. Origins of Life and Evolution of Biospheres 49, 163-185.

https://doi.org/10.1007/s11084-019-09582-9

In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino

acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.

Lazar, M., Gasperini, L., Polonia, A., Lupi, M., Mazzini, A., 2019. Constraints on gas release from shallow lake sediments—a case study from the Sea of Galilee. Geo-Marine Letters 39, 377-390.

https://doi.org/10.1007/s00367-019-00588-w

The presence of methane gas in the shallow sub-surface sediments of the Sea of Galilee, northern Israel, has been well documented over the years. Numerous theories for the mechanism responsible for the release of this gas into the water column have been put forth. These include changes in lake levels, seasonality, and seismic activity. The presence of gas in the sediments has been shown to cause acoustic blanking of the seismic signal. In effect, this means that areas of good seismic penetration are areas where gas is not present in the underlying sediment. In this study, 30 years of high-resolution seismic reflection data from the northwestern corner of the lake was examined. This database has allowed for the examination of changes in the spatial extent of gas in the area over time. Results show that the presence or absence of gas in the sediments does not adhere to one clear governing mechanism as previously assumed, but is rather a combination of factors that must be taken into account.

Le Nagard, L., Zhu, X., Yuan, H., Benzerara, K., Bazylinski, D.A., Fradin, C., Besson, A., Swaraj, S., Stanescu, S., Belkhou, R., Hitchcock, A.P., 2019. Magnetite magnetosome biomineralization in Magnetospirillum magneticum strain AMB-1: A time course study. Chemical Geology 530, 119348.


Magnetotactic bacteria are a highly studied group of diverse prokaryotes that biomineralize chains of magnetosomes, single domain, single crystal magnetic nanoparticles of magnetite or greigite, enclosed by a lipid bilayer membrane whose synthesis is under strict genetic control. In addition to characterizing the genetics and physicochemical properties of both cultured and uncultured environmental species, there have been a number of investigations using a time course approach to determine the chemical pathway of magnetite biomineralization in these organisms. In time course studies, cells of MTB are typically grown in the absence of iron so they cannot make magnetite, and then provided with iron in culture medium which initiates the biomineralization of magnetosome chains over a subsequent time period. Results from previous time course studies are not consistent with one another, differing with regard to the nature of chemical intermediates and the rate of establishment of magnetosome chains. In this work we report a time course study of Magnetospirillum magneticum strain AMB-1 over a 48 h (hour) period, using transmission electron microscopy (TEM) and soft X-ray scanning transmission X-ray microscopy (STXM) at the Fe L-edge. STXM provides capability to measure X-ray absorption spectra (XAS) and map chemical species with ∼25 nm spatial resolution and thus gives detailed results on the chemistry of individual particles in

single cells. An evolution of the iron oxide speciation, from a more Fe(III)-rich species, possibly α-hematite (Fe2O3), to magnetite (Fe3O4), was observed in the early stages, with evidence for the presence of the Fe(III)-rich character persisting up to 24 h. The spectromicroscopy (X-ray absorption, XAS and X-ray magnetic circular dichroism, XMCD) and TEM results show that biomineralization occurs in a stepwise fashion. First, very small particles, with no measurable magnetization, are produced at different sites in the cell without significant chain formation. The Fe L3 spectra of these early stage particles typically differ from magnetite with an additional signal at 708.4 eV that is consistent with α-hematite. By 6–8 h the particles are more numerous, partial chain formation is evident, and the L3 spectrum is very similar to that of magnetite. By 24 h particles-in-chains are the dominant motif and magnetism with the moment along the chain is established. By 48 h the cells are essentially the same as cells grown in Fe-rich medium.

Le Pichon, X., Şengör, A.M.C., İmren, C., 2019. Pangea and the lower mantle. Tectonics 38, 3479-3504.

https://doi.org/10.1029/2018TC005445

Abstract We show that the peripheral Pangea subduction zone closely followed a polar great circle. We relate it to the band of faster-than-average velocities in lowermost mantle. Both structures have an axis of symmetry in the equatorial plane. Assuming geologically long-term stationarity of the deep mantle structure, we propose to use the axis of symmetry of Pangea to define an absolute reference frame. This reference frame is close to the slab remnants and NNR frames of reference but disagrees with hot spot-based frames. We apply this model to the last 400 Myr. We show that a hemispheric supercontinent appeared as early as 400 Ma. However, at 400 Ma, the axis of symmetry was situated quite far south and progressively migrated within the equatorial plane that it reached at 300 Ma. From 300 to 110?100 Ma, it maintained its position within the equatorial plane. We propose that the stationarity of Pangea within a single hemisphere surrounded by subduction zones led to thermal isolation of the underlying asthenosphere and consequent heating as well as a large accumulation of hot plume material. We discuss some important implications of our analysis concerning the proposition that the succession of supercontinents and dispersed continents is controlled by an alternation from a degree 1 to a degree 2 planform.

Lee, D.-H., Lee, Y.M., Kim, J.-H., Jin, Y.K., Paull, C., Niemann, H., Kim, J.-H., Shin, K.-H., 2019. Discriminative biogeochemical signatures of methanotrophs in different chemosynthetic habitats at an active mud volcano in the Canadian Beaufort Sea. Scientific Reports 9, 17592.

https://doi.org/10.1038/s41598-019-53950-4

Several mud volcanoes are active in the Canadian Beaufort Sea. In this study, we investigated vertical variations in methanotrophic communities in sediments of the mud volcano MV420 (420 m water depth) by analyzing geochemical properties, microbial lipids, and nucleic acid signatures. Three push cores were collected with a remotely operated vehicle from visually discriminative habitats that were devoid of megafauna and/microbial mats (DM) to the naked eye, covered with bacterial mats (BM), or colonized by siboglinid tubeworms (ST). All MV420 sites showed the presence of aerobic methane oxidation (MOx)- and anaerobic methane oxidation (AOM)-related lipid biomarkers (4α-methyl sterols and sn-2-hydroxyarchaeol, respectively), which were distinctly different in comparison with a reference site at which these compounds were not detected. Lipid biomarker results were in close agreement with 16S rRNA analyses, which revealed the presence of

MOx-related bacteria (Methylococcales) and AOM-related archaea (ANME-2 and ANME-3) at the MV420 sites. 4α-methyl sterols derived from Methylococcales predominated in the surface layer at the BM site, which showed a moderate methane flux (0.04 mmol cm−2 y−1), while their occurrence was limited at the DM (0.06 mmol cm−2 y−1) and ST (0.01 mmol cm−2 y−1) sites. On the other hand, 13C-depleted sn-2-hydroxyarchaeol potentially derived from ANME-2 and/or ANME-3 was abundant in down-core sediments at the ST site. Our study indicates that a niche diversification within this mud volcano system has shaped distinct methanotrophic communities due to availability of electron acceptors in association with varying degrees of methane flux and bioirrigation activity.

Lee, H., Galy, V., Feng, X., Ponton, C., Galy, A., France-Lanord, C., Feakins, S.J., 2019. Sustained wood burial in the Bengal Fan over the last 19 My. Proceedings of the National Academy of Sciences 116, 22518-22525.


Significance: The Bengal Fan is the largest sedimentary deposit in the world and has previously been shown to represent a major sink of carbon that may have contributed to the Cenozoic cooling trend. Wood transport has been observed in rivers during the high flows of the monsoon season, or associated with events such as cyclones, earthquake-triggered landslide and dam-and-release events from the mountains. However, wood was not widely thought to survive export and burial in the oceans. This study shows that woody debris can survive thousands of kilometers of transport in rivers and in turbidites, to be deposited in the fan. Wood has been overlooked in quantification of organic carbon burial on continental margins.

Abstract: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.

Lee, J.S., Han, J.H., An, S.-U., Kim, S.-H., Lim, D., Kim, D., Kang, D.-J., Park, Y.-G., 2019. Sedimentary organic carbon budget across the slope to the basin in the southwestern Ulleung (Tsushima) Basin of the East (Japan) Sea. Journal of Geophysical Research: Biogeosciences 124, 2804-2822.

https://doi.org/10.1029/2019JG005138

Abstract With the total sediment oxygen uptake rates measured using an in situ benthic chamber, vertical distributions of organic carbon, and sedimentation rates estimated by excess 210Pb across the slope to the basin sediment of the southwestern region of the Ulleung (Tsushima) Basin (UB), the partitioning of organic carbon fluxes in the sediment was estimated to understand the biogeochemical cycles of organic carbon in the high productivity marginal sea. The results of depth attenuation of total oxygen uptake (TOU) demonstrate that the organic carbon oxidation of the UB sediment was 2.5 times higher than that obtained from the empirical relationship of the global's depth attenuation of TOU. Similar to TOU, the high mass accumulation rates observed in the slope region were 9.5 times higher than the rate in the basin, indicating that the slope may act as the depocenter of organic carbon. The organic carbon budget with water depth gradient implies that a significant fraction of the organic carbon deposited into sediment is supplied by lateral transport down the slope. Definite increasing C/N ratio with water depth indicates that the refractory organic carbon seems to be successively transported later from shelf to slope. The total burial flux in the sediment of southwestern UB was estimated to be 0.46±0.04 Tg C/year, which is similar to the megadepocenter of the Congo River fan. Our results imply that the UB sediment may be an important biogeochemical reaction place not only for organic carbon but also materials linked to primary production.

Lei, H., Zhang, Q., Li, X., 2019. Preliminary numerical modeling of CO2 geological storage in the Huangcaoxia gas reservoir in the eastern Sichuan Basin, China. Geofluids 2019, 9545723.

https://doi.org/10.1155/2019/9545723

Depleted gas reservoirs are important potential sites for CO2 geological sequestration due to their proven integrity and safety, well-known geological characteristics, and existing infrastructures and wells built for natural gas production. The Sichuan Basin has a large number of gas fields in which approximately tons of CO2 can be stored. The Huangcaoxia gas field has the best opportunity in the eastern Sichuan Basin for a pilot project of CO2 sequestration due to its relatively large storage capacity and the nearly depleted state. A coupled thermal-hydrodynamic model including faults is built based on the geological and hydrogeological conditions in the Huangcaoxia gas field. The results of the numerical simulations show that the downhole temperature is above 80°C at a downhole pressure of 14 MPa under the constraint of temperature drop in the reservoir due to the strong Joule-Thomson effect. The corresponding injection pressure and temperature at the wellhead are 10.5 MPa and 60°C, respectively. The sizes of the pressure and CO2 plumes after an injection of 10 years are 18 km and 5 km, respectively. The zone affected by temperature change is very small, being about 1-2 km away from the injection well. The injection rate in the injection well Cao 31 averages 6.89 kg/s ( tons/a). For a commercial-scale injection, another four wells (Cao 9, Cao 30, Cao 6, and Cao 22) can be combined with the Cao 31 well for injection, approaching an injection rate of 35 kg/s ( tons/a). Both the pressure and temperature of CO2 injection decrease with the increasing depleted pressure in the gas reservoir when the latter is below 6 MPa. With the technique of CO2-enhanced gas recovery (CO2-EGR), the CO2 injection rate is improved and approximately of gas can be produced during a studied time period of 10 years.

Lei, L., Seol, Y., Myshakin, E.M., 2019. Methane hydrate film thickening in porous media. Geophysical Research Letters 46, 11091-11099.

https://doi.org/10.1029/2019GL084450

Abstract:

Methane hydrate formation accompanied by upward migration of methane in sediments was studied. Methane hydrate film forms initially along the interface between the gas and surrounding pore fluid when methane reaches the hydrate stability zone. Subsequent film thickening and related mass transfer are critical but have not been studied previously. Experimental and theoretical studies were performed to investigate the film thickening and rate limiting mechanisms. Initial gas density ‐affects the stability of the growing hydrate film, and mass transfer through hydrate film is proposed as a rate limiting step for hydrate growth.‐

Plain Language Summary:

Gas hydrate films can quickly form when gas and water meet each other given proper pressure and temperature. Yet, little is known about what occurs afterward. We use both experimental and theoretical approaches to investigate slow transformation of methane bubbles to methane hydrate. Two experiments were conducted using gas densities lower or higher than methane density in methane hydrate. In the lower density case, the initially formed hydrate film breaks, which lets ‐water invade into the gas bubble. By contrast, the hydrate film maintains its integrity in the higher‐density case, and the slowly formed hydrate takes over both the spaces initially occupied by gas and water. Observations indicate that both water transfer into the gas bubble and outward gas transfer from the bubble occur through hydrate films. A theoretical analysis explores these processes based on the slow mass migration via seemingly solid hydrate: (1) gas diffusion driven by gas concentration gradient in hydrate and (2) water flow via conduits within polycrystalline hydrate driven by pressure gradients. The mass transfer rates match experimental observations and agree with previous studies. Results suggest that natural hydrate formed from free gas at significant depth could have residual gas inclusions for millions of years.



The D/H ratio imaging of weakly hydrated minerals prepared as focused ion beam (FIB) sections is developed in order to combine isotopic imaging by nanoscale secondary ion mass spectrometry (NanoSIMS) of micrometer-sized grains with other nanoscale imaging techniques, such as transmission electron microscopy. In order to maximize the accuracy, sensitivity, precision, and reproducibility of D/H ratios at the micrometer size, while minimizing the surface contamination at the same time, we explored all instrumental parameters known to influence the measurement of D/H ratios in situ. Optimal conditions were found to be obtained with the use of (i) a Cs+ ion source and detection of H– and D– at low mass resolving power, (ii) a primary beam intensity of 100 pA, and (iii) raster sizes in the range of 8–15 μm. Nominally anhydrous minerals were used to evaluate the detection limits and indicate a surface contamination level of ∼200 ppm equivalent H2O under these conditions. With the high primary intensity used here, the dwell time is not a parameter as critical as found in previous studies and a dwell time of 1 ms/px is used to minimize dynamic contamination during analysis. Analysis of FIB sections was found to reduce significantly static contamination due to sample preparation and improved accuracy compared to using polished sections embedded not only in epoxy but in indium as well. On amphiboles, the typical overall uncertainty including

reproducibility is ∼20 ‰ on bulk FIB sections and ∼50 ‰ at the 1.5 μm scale using image processing (1σ).

Li, D.-D., Wang, J., Wan, S., Pšenička, J., Zhou, W.-M., Bek, J., Votočková-Frojdová, J., 2019. A marattialean fern, Scolecopteris libera n. sp., from the Asselian (Permian) of Inner Mongolia, China. Palaeoworld 28, 487-507.


Scolecopteris libera n. sp. is established on partial three-dimensionally preserved materials containing both sterile and fertile fronds collected from the volcanic tuff at the top of the Taiyuan Formation at the Wuda Coalfield, Inner Mongolia, China. It is characterized by tripinnate fronds with rachises over 200 mm in diameter; and long lanceolate or falciform pinnules with thick veins. Pinnules are of the pecopterid-type, with those at the base of the ultimate pinnae usually divided into small lobes. Eight to twelve circular synangia are arranged in two rows along the midvein. Synangia are borne on a short pedicel attached to the middle of lateral veins. A synangium is composed of 7–10 fusiform exannulate sporangia with pointed apices. The sporangia are free among each other beyond the base of synangia. In situ microspores of the Cyclogranisporites leopoldii type differ from all other in situ Paleozoic marattialean spores.



Phenolic moieties are important constituents in dissolved organic matter (DOM) in natural and engineered systems. However, their roles in membrane fouling mechanism during drinking water treatment by ultrafiltration (UF) have remained elusive. Herein, by using water insoluble polyvinylpolypyrrolidone (PVPP) resins, we sequestered the phenolic moieties from a model DOM (Suwannee River DOM, SRDOM) and characterized their molecular profiles using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Subsequently, their roles in UF membrane fouling propensity were investigated using reconstituted DOM solutions with various concentrations of phenolic moieties. The results showed that the phenolic moieties were of higher molecular weight and rich in unsaturation cyclic structures and oxygen-rich groups. Van Krevelen diagrams revealed that the sequestered sample was rich in aromatics structures and tannins-like compounds while contained less alicyclic organic acids in comparison with the original SRDOM, which was consistent with the aromaticity index (AI) analysis. UF experiments showed that the more phenolic moieties in DOM solution, the severer decline of flux was observed. The phenolic moieties played a significant role in membrane irremovable fouling due to the hydrophobic interactions and their higher molecular weight as evidenced by membrane cleaning tests. By surface characterization, the SRDOM fouled membrane was identified to have a higher water contact angle value and abundant C–O groups, likely due to the adsorption of more hydrophobic phenolic moieties. Overall, these findings highlighted links between phenolic moieties and membrane fouling development, and implied that membrane performance could be improved by pre-removal of phenolic moieties in DOM.

Li, H.-C., Wang, J., Sun, J.-J., Chou, C.-Y., Li, H.-K., Xia, Y.-Y., Zhao, H.-Y., Yang, Q.-N., Kashyap, S., 2019. Study of Jinchuan Mire in NE China I: AMS 14C, 210Pb and 137Cs dating on peat cores. Quaternary International 528, 9-17.


This paper presents dating results of AMS 14C, 210Pb and 137Cs methods on two young peat profiles from Jinchuan Mire in southeast Jilin of China. JC1 (50-cm long) from a hummock of the mire covers 1962–2007 CE with an accumulation rate of 1.12 cm/y, whereas JCA (92-cm long) from a lawn site involves a 1000-year record with a mean sedimentation of 0.09 cm/y. Comparison of the dating results of the last 100-y part of the peat cores, chronologies based on the AMS 14C dating are most reliable, because the mobility of 210Pb and 137Cs in peat profiles causes overestimation of depositional rate with the larger errors in the deeper layers. The F14C of peat samples were significantly lower than that of the atmospheric CO2 for the post nuclear bomb period because of three reasons: (1) uptake of old CO2 dissolved in the water by aquatic plants during photosynthesis; (2) long-term mixing of the atmospheric CO2 in multiple year growth of the plants; and (3) perhaps dilution effect caused by strong surface runoff. Among these factors, Factor (1) accounts for the major influence. Hence, a “bomb 14C curve” from a peat profile is necessary for determining post bomb ages. For the pre-nuclear bomb ages, acid-base-acid (ABA) treatment of a peat sample may cause an older-than-true age due to removal of organic acids produced during photosynthesis. This observation calls for detailed investigation of mechanism study and proper pretreatment of peat samples for 14C dating. The large difference of the depositional rates in the same peatland between JC1 and JCA indicates that estimation of carbon storage in a peatland should be based on the database of multiple sites rather than a couple of cores. For the same reason, one should not use a depositional rate either from a core with distance in the same peatland or from an adjacent peatland.

Li, J., Wang, M., Chen, Z., Lu, S., Jiang, C., Chen, G., Tian, S., 2019. Evaluating the total oil yield using a single routine Rock-Eval experiment on as-received shales. Journal of Analytical and Applied Pyrolysis 144, 104707.


Shales in the early maturity and oil window stages contain a considerable amount of heavy hydrocarbons (S2oil) having strong interactions with kerogen/rock that make the accurate measurement of total oil (total extractable organic matter) more difficult from the routine Rock-Eval experiment. In this study, a fast method for evaluating the total oil yield using a single routine Rock-Eval experiment on as-received shales is proposed. First, the temperature threshold (TOK) of the S2oil and cracking hydrocarbons were determined by combining the pyrograms of the as-received shale with a solvent-extracted replicate. Then, the total oil yield was directly derived from the hydrocarbons evaporate at a temperature below than TOK in a routine Rock-Eval experiment. The results show that the TOK value is controlled by the sample’s maturity and pore structure. The higher the maturity, the larger the specific surface area and the smaller the pore size, the greater the TOK. A prediction model of TOK was proposed based on the sample’s production index (PI). The total oil yields estimated by the two methods of both the TOK prediction model and the average TOK value (465 °C) are consistent with those obtained by Jarvie (2012) using the thermal-extraction method with correlation coefficients of 0.983 and 0.9548, respectively. Compared with the previous methods, the single routine Rock-Eval experiment method proposed in this study is convenient and not requires an extraction experiment. In addition, there are archived routine pyrolysis data

available that can be used to directly calculate the total oil yield based on the temperature threshold.

Li, J., Wang, M., Lu, S., Chen, G., Tian, W., Jiang, C., Li, Z., 2020. A new method for predicting sweet spots of shale oil using conventional well logs. Marine and Petroleum Geology 113, 104097.


In this paper, a new method called sweet spot index (SSI) is proposed by the combination of shale oil mobility and shale reservoir fracability to predict the vertical distribution of shale oil sweet spots using conventional logs. In the SSI method, logging evaluation models for TOC, S1 (volatile petroleum), and mineral content are initially established. Mobile oil content is obtained by subtracting the amount of adsorbed oil from the total oil content, which is the S1 value after the recovery of light and heavy hydrocarbons. The adsorbed oil content is calculated based on the oil adsorption model established by a stepwise pyrolysis experiment. The formation fracability is estimated by a combination of estimates of brittle mineral content and Young's modulus. Formations with higher brittleness and lower Young's modulus are considered better simulation candidates. The SSI value is the product of the normalized mobility and the fracability index, which minimizes the section of just an organic matter sweet spot (i.e., high oil content) or an inorganic sweet spot (i.e., easily fractured) and has the advantage of accurately predicting its vertical distribution. In the case study, the new method is successfully implemented to predict sweet spots of the Es3L (lower sub member of the third member of the Eocene Shahejie Formation) in the Bonan Sag, Bohai Bay Basin, China. The lower limit value of SSI is set to 0.1 based on its relationship with shale oil production. The effectiveness, reliability and adaptability of the SSI method have been verified by three wells in the Bonan Sag.

Li, J., Wang, Q.-L., Liu, Y., Ke, Y., Fan, Q.-Q., Zhou, P., An, M.-C., Liu, H.-M., 2019. Simultaneous determination of 24 free amino acids in MGC803 cells by hydrophilic interaction liquid chromatography with tandem mass spectrometry. Journal of Chromatography B 1132, 121792.


Amino acids play key roles in cellular protein biosynthesis and energy metabolism pathways. In this study, a simple, rapid and sensitive method was developed for the simultaneous determination of 24 free amino acids in cell samples using hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry (HILIC-MS/MS). Cell samples were deproteinized with methanol/H2O (80:20, v/v) without intricate derivatization process. The analytes were separated on a Waters BEH Amide column (2.1 mm × 100 mm, 1.7 μm), and accomplished within 5 min at a flow rate of 0.2 mL/min. The good linearity was obtained for all analytes (r2 > 0.99) with the limits of quantification from 0.1 to 25 ng/mL. The intra- and inter-day precision ranged from 0.35 to 10.36% and from 2.22 to 9.93%, respectively. The recoveries of most analytes were between 80% and 120% with RSD less than 10.0%. The developed method was then applied to the direct analysis of 24 underivatized amino acids in human gastric cancer cell line MGC803 treated with the antitumor candidate drug J3, and significant differences in the concentration levels of amino acids were also assessed.



Atomic-scale structural transformation of coke carbon in the thermal annealing process was investigated with four coke carbon samples using X-ray diffraction, Raman spectroscopy, X-ray photoemission spectroscopy, and ReaxFF molecular dynamics. Microcrystal graphite was confirmed to be the basic structural unit in coke carbon structure, and its average size increased from (Lc: 23–27 Å; La: 48–50 Å) to (Lc: 53–78 Å; La: 53–63 Å) with increasing annealing temperature. The coke carbon structural evolution in 1300–1500 °C is not Raman-sensitive because most coke carbon bonding types were found to be sp2 with a stable content (>60%). ReaxFF simulation repeated the experimental results very well and indicates that it is relatively hard to form a well-structured order in the graphene plane (La) direction compared with that in the vertical direction (Lc). Five-membered carbon rings, especially when two five-membered rings are connected together, make the graphene layers curved to some extent, leading to the formation of defects as well as disorder in the graphene plane. The increase of carbon structural order decreases the carbon reactivity with CO2, but a clear correlation cannot be constructed in the present study since some other factors such as nanopores and residue ash may also influence coke reactivity.

Li, L., Zhong, S., Shen, X., Li, Q., Xu, W., Tao, Y., Yin, H., 2019. Recent development on liquid chromatography-mass spectrometry analysis of oxidized lipids. Free Radical Biology and Medicine 144, 16-34.


Polyunsaturated fatty acids (PUFAs) in the cellular membrane can be oxidized by various enzymes or reactive oxygen species (ROS) to form many oxidized lipids. These metabolites are highly bioactive, participating in a variety of physiological and pathophysiological processes. Mass spectrometry (MS), coupled with Liquid Chromatography, has been increasingly recognized as an indispensable tool for the analysis of oxidized lipids due to its excellent sensitivity and selectivity. We will give an update on the understanding of the molecular mechanisms related to generation of various oxidized lipids and recent progress on the development of LC-MS in the detection of these bioactive lipids derived from fatty acids, cholesterol esters, and phospholipids. The purpose of this review is to provide an overview of the formation mechanisms and technological advances in LC-MS for the study of oxidized lipids in human diseases, and to shed new light on the potential of using oxidized lipids as biomarkers and mechanistic clues of pathogenesis related to lipid metabolism. The key technical problems associated with analysis of oxidized lipids and challenges in the field will also discussed.

Li, M., Chen, Z., Qian, M., Ma, X., Jiang, Q., Li, Z., Tao, G., Wu, S., 2020. What are in pyrolysis S1 peak and what are missed? Petroleum compositional characteristics revealed from programed pyrolysis and implications for shale oil mobility and resource potential. International Journal of Coal Geology 217, 103321.


This article presents a novel numerical decomposition method based on generation kinetics for studying oil composition characteristics from S1 peak of single heating rate pyrolysis of source rock samples. Furthermore, phase behavior and PVT analysis were introduced in the calculation to make a full correction for evaporative loss of gaseous and light hydrocarbon in S1 during coring and sample storage. Special programed pyrolysis results of twenty-eight core samples, along with a routine source rock screening pyrolysis dataset of 68 samples, from a recent shale oil study well of the Eocene Qianjiang Formation in Jianghan Basin, China were analyzed to demonstrate the application of proposed methods. We showed that (a) by reassembling corresponding activation energies, the original S1 curve can be split into groups of similar thermal evaporative property, resulting in a composition classification of free hydrocarbons in S1 when it was converted back to temperature domain; (b) a full correction on the gaseous and light hydrocarbon loss in S1 permits a more precise estimation of oil composition as well as total resource; (c) the resulting oil composition grouping provides information for inferring the fraction of extractable hydrocarbon; d) oil composition varies considerably among the samples within a stratigraphic interval of 20 m. Samples from intra salt organic-rich lamina show different compositional characteristics with much less abundance in gaseous and volatile oil compounds; while samples from inter salt interval contain large portion of volatile and light oil, indicating a promising production zone.

Li, Y., Chen, S., Lu, J., Wang, G., Zou, X., Xiao, Z., Su, K., He, Q., Luo, X., 2020. The logging recognition of solid bitumen and its effect on physical properties, AC, resistivity and NMR parameters. Marine and Petroleum Geology 112, 104070.


Solid bitumen not only strongly damages the reservoir properties, but it is easily confused with oil and gas in the conventional classification logging interpretation, which seriously affects the effective recognition of oil and gas. Thus, it leads to a deceptive estimation of the reserve. Focusing on the above problems, this study takes Jurassic solid bitumen-containing reservoirs from the Santai-Northern Santai area in the Junggar Basin as an example, and aims to quantitatively evaluate the impact of solid bitumen on the porosity, permeability, resistivity, AC (Acoustic) and NMR (Nuclear Magnetic Resonance), with a comparison between the values of these parameters before and after core bitumen dissolution, as well as to establish an NMR identification method for solid bitumen. The results show that solid bitumen can damage the pore structure of the reservoir and cause a reduction of porosity and permeability. The content of solid bitumen is linearly correlated with the change of porosity and permeability. After solid bitumen dissolved, the resistivity decreased, the longitudinal wave time difference (Vp) and shear wave time difference (Vs) increased, and the shear wave time difference changed noticeably. The content of solid bitumen is exponentially correlated with the change of resistivity, and linearly correlated with the change of longitudinal wave time difference and shear wave time difference. Solid bitumen had a short transverse relaxation time and a response range of 10–1000 μs (Peak 1) on the T2 map. Bitumen-containing sandstone had 3 peaks on the T2 map. Peak 1 decreased, while Peaks 2 and 3 increased after the solid bitumen dissolved. Solid bitumen can be characterized by a typical short time lag of the transverse wave, a bigger density porosity than the NMR porosity and small values of T1LM and T2LM, which led to an effective recognition of the layers of solid bitumen. The results are significant for the exploration and development of oilfields.

Li, Z.-H., Yan, F., Ketcham, R.A., Colbert, M.W., Clarke, J.A., 2019. Mass-transfer based modeling to investigate iodine staining effects for enhanced contrast X-ray computed tomography. Palaeoworld 28, 562-571.


Iodine staining combined with X-ray computed tomography (CT) has become a core approach in anatomy, offering three-dimensional and essentially non-destructive imaging of soft tissues. Although there have been rapid advances in methodologies and techniques, the mechanisms underlying diffusible iodine contrast-enhanced CT are not yet fully understood. The protocols for staining samples of differing sizes and tissue types have not yet been justified theoretically. Here we utilize mass transfer modeling to simulate iodine diffusion and predict iodine concentrations within distinct tissue types. We also undertake iodine staining experiments to visualize the detailed anatomy and contrast effects on whole-body avian specimens using different concentrations of iodine solution to compare with model simulation results. The simulations effectively explain most observed concentration changes in differently-sized samples over distinct iodine treatment durations. These results also provide insight into the mechanisms behind the efficacy of solution replenishment for enhancing staining effects. Both consistencies and inconsistencies between our simulation and experimental results regarding iodine concentration in tissues will inform further investigations to optimize iodine staining protocols.

Li, Z., Ni, G., Sun, L., Sun, Q., Li, S., Dong, K., Xie, J., Wang, G., 2020. Effect of ionic liquid treatment on pore structure and fractal characteristics of low rank coal. Fuel 262, 116513.


In order to study the variation of pore characteristics and fractal dimensions, coal samples are treated by ionic liquid with different concentrations. Then the N2 isotherm adsorption/desorption experiment is carried out. The results show that water treatment caused a decrease in total pore volume. While the total pore volume in ionic liquid treated coal samples are larger than that in water treated coal sample. In comparison with water treated coal sample, the volumes of micropores in ionic liquid treated coal samples are reduced and the specific surface areas are increased. However, the volume and specific surface area of the mesopores are opposite to those in the water treated coal sample. The fractal dimensions D1 and D2 are calculated. The results show D1 decreases in water treated coal sample while increases in ionic liquid treated coal samples. D2 decreases obviously in water treated coal sample. Besides, it is lower than that in ionic liquid treated coal samples. Those indicate single water treatment will decrease the surface roughness and structural complexity of pores, while ionic liquid treatment will increase it. This study is of great significance to enhance the CBM exploitation and reduce the water block effect.

Li, Z., Qiu, N., Liu, N., Cai, C., Tian, J., Wang, Y., Gao, T., Gu, Q., 2019. Applying quantitative fluorescence techniques to characterize mechanism of hydrocarbon migration and accumulation in thick source strata: a case study of Member 4 of Shahejie Formation, Langgu sag in Bohai Bay Basin Acta Petrolei Sinica 40, 1158-1171.

http://www.syxb-cps.com.cn/EN/abstract/abstract5762.shtml

Due to the influence of heterogeneity and effective hydrocarbon expulsion thickness, the mechanism of hydrocarbon migration in thick source strata is still not clear, directly affecting the evaluation of petroleum resources quantity and the establishment of hydrocarbon accumulation model in the basin. The quantitative fluorescence analysis includes a series of techniques including quantitative grain fluorescence (QGF), quantitative grain fluorescence on extract (QGF-E), and total scanning fluorescence (TSF), which can accurately provide such important information as hydrocarbon saturation, maturity and migration path during the past and present geological periods in a fast, simple, economical and efficient way. Using the quantitative fluorescence technique and basin simulation technique, this paper analyzes the hydrocarbon migration characteristics and charging history in the thick source strata of Member 4 of Shahejie Formation in Langgu sag, and also reconstructs the hydrocarbon migration and accumulation process from thick source strata to reservoirs. The results show that the QGF index of sandstone interlayers in thick source strata is generally greater than 4.0, the QGF-E intensity is partially greater than 40, and the λmax of QGF and QGF-E are quite different. It is indicated that paleo-oil layers once existed in the sand body were diluted and transferred in the later stage; the sand body played the role of "transfer station" during hydrocarbon migration and accumulation. The difference in quantitative fluorescence response indicates that the transit capacity of sand body varies at different depths. The coarser the lithology of sand body is, the more closely the sand ratio approaches to 0.25; the thicker the sand body is, the higher the migration efficiency is, and the larger the transit capacity is. The hydrocarbon generation and thermal evolution histories of source rocks, quantitative fluorescence spectra of sand strata and fault activity histories demonstrate that there are two episodic hydrocarbon transport and accumulation processes in the "transfer station". The first stage is from the end stage of Member 3 of Shahejie Formation to the early stage of Dongying Formation (35-30 Ma). The sand body was mainly filled with medium-light oil and gas. With the opening of faults, oil and gas migrated upward efficiently from the end stage of Member 1 of Shahejie Formation to the early stage of Dongying Formation. When hydrocarbon generation ceased at the end stage of Dongying Formation, the oil and gas saturation in the sand body was decreased. The second stage is from the sedimentary period of Minghuazhen Formation to the present (5-0 Ma). The sand body is mainly charged with a large amount of condensate oil and gas. Since the faults tend to be closed, the oil and gas in the sand body migrate upward by steady seepage; till the formation of better preservation conditions, oil and gas can be accumulated in the buried hill reservoir.

Liang, D., Li, M., Wei, R., Wang, J., Li, Y., Jia, W., Chen, T., 2019. Strategy for intercorrelation identification between metabolome and microbiome. Analytical Chemistry 91, 14424-14432.


Accumulating evidence points to the strong and complicated associations between the metabolome and the microbiome, which play diverse roles in physiology and pathology. Various correlation analysis approaches were applied to identify microbe–metabolite associations. Given the strengths and weaknesses of the existing methods and considering the characteristics of different types of omics data, we designed a special strategy, called Generalized coRrelation analysis for Metabolome and Microbiome (GRaMM), for the intercorrelation discovery between the metabolome and microbiome. GRaMM can properly deal with two types of omics data, the effect of confounders, and both linear and nonlinear correlations by integrating several complementary methods such as the classical linear regression, the emerging maximum information coefficient (MIC), the metabolic confounding effect elimination (MCEE), and the centered log-ratio transformation (CLR). GRaMM

contains four sequential computational steps: (1) metabolic and microbial data preprocessing, (2) linear/nonlinear type identification, (3) data correction and correlation detection, and (4) p value correction. The performances of GRaMM, including the accuracy, sensitivity, specificity, false positive rate, applicability, and effects of preprocessing and confounder adjustment steps, were evaluated and compared with three other methods in multiple simulated and real-world datasets. To our knowledge, GRaMM is the first strategy designed for the intercorrelation analysis between metabolites and microbes. The Matlab function and an R package were developed and are freely available for academic use (comply with GNU GPL.V3 license).

Liang, J., Zhang, W., Lu, J.a., Wei, J., Kuang, Z., He, Y., 2019. Geological occurrence and accumulation mechanism of natural gas hydrates in the eastern Qiongdongnan Basin of the South China Sea: Insights from site GMGS5-W9-2018. Marine Geology 418, 106042.


Seismic and logging while drilling (LWD) data, gas hydrate samples, and hydrate gas geochemical testing results acquired during the GMGS5 expedition in 2018 have been used to explore the geological occurrence and accumulation mechanism of gas hydrates in the eastern Qiongdongnan Basin (QDNB) of the northern South China Sea (SCS). A large gas chimney with diameter of 4 km associated with the Songnan Low Uplift and the Central Channel and characterized by acoustic blanking on the seismic profile was identified at site GMGS5-W9-2018 in the deep water QDNB. Seismic indications for hydrocarbon migration and gas hydrate accumulation including low frequency features, enhanced reflections, pull-ups/downs and the bottom simulating reflector (BSR) were recognized within the chimney area. Gas hydrates were confirmed to be deposited at the depth of 7–158 mbsf based on the coring and sampling results and pilot hole LWD anomalies, which showed a high resistivity, low density, high gamma rays, and elevated acoustic velocity. Leakage type gas hydrates with multiple geomorphology occurrence, including massive, layers, nodules, fracture filling and disseminated, were recovered at the top of the gas chimney, suggesting favorable conditions for the accumulation of gas hydrates in the eastern QDNB. Although methane was the dominant hydrocarbon gas in all hydrate-bound gases, heavier hydrocarbons (C2+) were also prevalent. C2–C5 hydrocarbons made up to ~21% of the hydrocarbon gases, indicating their thermogenic origin and close relationship with deep reservoirs. Due to the presence of the C2+ hydrocarbons, structure I and structure II gas hydrates may coexist at site GMGS5-W9-2018. The base of structure II gas hydrate stability zone (BSIIGHSZ) was ~42–44 m deeper than the base of structure I gas hydrate stability zone (BSIGHSZ). The hydrocarbon migration and hydrate accumulation were closely related to the gas chimney in conjunction with the Songnan Low Uplift and the Central Channel, which transported the deep thermogenic gas to the GHSZ, forming hydrates in the fractured clay-dominated fine-grained sediments. The fractures occurred in the strata were likely driven by pneumatic forces. Overpressure in the sediments derived from gas charging and accumulation through the gas chimney may have caused the fractures in the sediments that dissipated the hydrocarbons into the GHSZ. We propose a model of gas hydrate accumulation that may aid in the future exploration of gas hydrates in the QDNB of the SCS.

Liao, Z., Hu, W., Cao, J., Wang, X., Fu, X., 2020. Oceanic anoxia through the late Permian Changhsingian Stage in the Lower Yangtze region, South China: Evidence from sulfur isotopes and trace elements. Chemical Geology 532, 119371.


The late Permian oceanic anoxic event is suggested to have had a causal relationship with the Latest Permian Mass Extinction (LPME); however, the nature of spatio-temporal variations in the anoxic event prior to the LPME remains poorly known. Here we provided new constraints on this issue based on high-resolution geochemical analyses of sulfur isotopes and trace elements in the Niushan section (nearby the Meishan section) of the Lower Yangtze region, South China. Results show that the entire Upper Permian Changhsingian in the study area can be divided into five intervals according to organic carbon isotope evolutionary trend. From the bottom to top, the water was oxic (interval I) to anoxic with sporadically euxinic condition (interval II) to primarily suboxic (interval III) to anoxic with frequently euxinic condition (interval IV), to a transient euxinic event (interval VEH) under dysoxic/oxic conditions (interval V). Multiple productivity proxies (total organic carbon, Cuxs, and Znxs) suggest that the primary productivity may have experienced a stable low (interval I), then was enhanced but with strong fluctuations (interval II), followed by a transient sharp decline (interval III), and was then subsequently relatively high with small fluctuations (interval IV), and finally experienced a gradual decline with occasional peaks (interval V) through the time interval represented by the Niushan section. The relationship between redox changes and paleoproductivity supports that a redox-stratified late Permian Ocean was present in the eastern Tethys region. Combined with previous results in South China, we propose that all the deep-water sections in the northern marginal basin of the Yangtze Platform (NMBY) might display similar trends, indicating that the NMBY was part of a single paleo-ocean system during the Changhsingian, although the Niushan section records more severely euxinic benthic water. The transient euxinic event during interval extinction horizon (VEH) can be well correlated with other sections worldwide, suggesting that the end-Permian marine anoxia in the Niushan section represents a global signal. The extinction horizon accompanied by a single euxinic episode in this study provides further evidence for the LPME having been caused by widespread anoxia. The bio-environmental evolutionary history of this continuous deep-water section will help us to better evaluate the data for the nearby shallow-water Meishan section.

Liebrand, D., de Bakker, A.T.M., 2019. Bispectra of climate cycles show how ice ages are fuelled. Climate of the Past 15, 1959-1983.

https://www.clim-past.net/15/1959/2019/

The increasingly nonlinear response of the climate–cryosphere system to insolation forcing during the Pliocene and Pleistocene, as recorded in benthic foraminiferal stable oxygen isotope ratios (δ18O), is marked by a distinct evolution in ice-age cycle frequency, amplitude, phase, and geometry. To date, very few studies have thoroughly investigated the non-sinusoidal shape of these climate cycles, leaving precious information unused to further unravel the complex dynamics of the Earth's system. Here, we present higher-order spectral analyses of the LR04 δ18O stack that describe coupling and energy exchanges among astronomically paced climate cycles. These advanced bispectral computations show how energy is passed from precession-paced to obliquity-paced climate cycles during the Early Pleistocene (from ∼2500 to ∼750 ka) and ultimately to eccentricity-paced climate cycles during the Middle and Late Pleistocene (from ∼750 ka onward). They also show how energy is transferred among many periodicities that have no primary astronomical origin. We hypothesise that the change of obliquity-paced climate cycles during the mid-Pleistocene transition (from ∼1200 to ∼600 ka), from being a net sink into a net source of energy, is indicative of the passing of a land-ice mass loading threshold in the Northern Hemisphere (NH), after which

cycles of crustal depression and rebound started to resonate with the ∼110 kyr eccentricity modulation of precession. However, precession-paced climate cycles remain persistent energy providers throughout the Late Pliocene and Pleistocene, which is supportive of a dominant and continuous fuelling of the NH ice ages by insolation in the (sub)tropical zones, and the control it exerts on meridional heat and moisture transport through atmospheric and oceanic circulation.

Lin, J.-P., Sundberg, F.A., Jiang, G., Montañez, I.P., Wotte, T., 2019. Chemostratigraphic correlations across the first major trilobite extinction and faunal turnovers between Laurentia and South China. Scientific Reports 9, 17392.

https://doi.org/10.1038/s41598-019-53685-2

During Cambrian Stage 4 (~514 Ma) the oceans were widely populated with endemic trilobites and three major faunas can be distinguished: olenellids, redlichiids, and paradoxidids. The lower–middle Cambrian boundary in Laurentia was based on the first major trilobite extinction event that is known as the Olenellid Biomere boundary. However, international correlation across this boundary (the Cambrian Series 2–Series 3 boundary) has been a challenge since the formal proposal of a four-series subdivision of the Cambrian System in 2005. Recently, the base of the international Cambrian Series 3 and of Stage 5 has been named as the base of the Miaolingian Series and Wuliuan Stage. This study provides detailed chemostratigraphy coupled with biostratigraphy and sequence stratigraphy across this critical boundary interval based on eight sections in North America and South China. Our results show robust isotopic evidence associated with major faunal turnovers across the Cambrian Series 2–Series 3 boundary in both Laurentia and South China. While the olenellid extinction event in Laurentia and the gradual extinction of redlichiids in South China are linked by an abrupt negative carbonate carbon excursion, the first appearance datum of Oryctocephalus indicus is currently the best horizon to achieve correlation between the two regions.

Lin, J.-S., Uchida, S., Myshakin, E.M., Seol, Y., Rutqvist, J., Boswell, R., 2019. Assessing the geomechanical stability of interbedded hydrate-bearing sediments under gas production by depressurization at NGHP-02 Site 16. Marine and Petroleum Geology 108, 648-659.


Establishing the geomechanical stability of marine sediments in the vicinity of a production well is one of the key design considerations in planning offshore gas production from marine hydrate reservoirs. This paper presents an assessment of the sediment stability at India's National Gas Hydrate Program, Expedition 2 (NGHP-02) Site 16 Area B offshore eastern India, for which gas production is to be carried out by depressurization. One important feature of the study is that extensive calibration of constitutive model parameters has been conducted based on laboratory test data from pressured core samples. From analysis perspective, the site is challenging because the hydrate reservoir consists of thin layers of hydrate-bearing sands interbedded with mud. Moreover, depressurization at the depth of a reservoir more than 2750 m below sea surface will lead to a pore pressure drop, and accordingly an effective confining stress increase as high as 25 MPa. In dealing with thin interbedded hydrate-bearing strata, meshing requirements for flow and geomechanical analysis are quite different from those for reservoirs with thicker massive layers, An axisymmetric model and one-way coupling simulations were thus adopted for this study, in which the geomechanical study utilizes pore pressure and hydrate saturation output from the flow study, but

the flow study does not takes the porosity changes from the geomechanical analysis. Instead, the reduction of porosity due to sediment deformation in the flow study is based on a pressure-dependent pore compressibility relationship derived from geomechanical modeling. The rationality is validated through back computing the pore compressibility from the geomechanical deformation results. The study shows that large compression in the reservoir will result in movement of the sediments from above and below, as well as laterally in smaller magnitudes; and the sediment is deemed stable during the gas production period.


https://doi.org/10.1111/maps.13381

A carbon rich melt fragment from the Gardnos impact structure has been studied for a better ‐understanding of the preservation and structural form(s) of carbon that have been processed by impact melting. The carbon was analyzed in situ in its original petrographic context within the melt fragment, using high resolution techniques including focused ion beam transmission electron ‐ ‐microscopy and electron energy loss spectroscopy. Results show that the carbon is largely uniform and has a nanocrystalline grain size. The Gardnos carbon has a graphitic structure but with a large c/a ratio indicating disorder. The disorder could be a result of rapid heating to high temperatures during impact, followed by rapid cooling, with not enough time to crystallize into highly ordered graphite. However, temperature distribution during impact is extremely heterogenous, and the disordered Gardnos carbon could also represent material that avoided extreme temperatures, and thus, it was preserved. Understanding the structure of carbon during terrestrial impacts is important to help determine if the history of carbon within extraterrestrial samples is impact related. Furthermore, the degree of preservation of carbon during impact is key for locating and detecting organic compounds in extraterrestrial samples. This example from Gardnos, together with previous studies, shows that not all carbon is lost to oxidation during impact but that impact melting can encapsulate and preserve carbon where it is available.

Lingam, M., Loeb, A., 2019. Role of stellar physics in regulating the critical steps for life. International Journal of Astrobiology 18, 527-546.

https://doi.org/10.1017/S1473550419000016

We use the critical step model to study the major transitions in evolution on Earth. We find that a total of five steps represents the most plausible estimate, in agreement with previous studies, and use the fossil record to identify the potential candidates. We apply the model to Earth-analogs around stars of different masses by incorporating the constraints on habitability set by stellar physics including the habitable zone lifetime, availability of ultraviolet radiation for prebiotic chemistry, and atmospheric escape. The critical step model suggests that the habitability of Earth-analogs around M-dwarfs is significantly suppressed. The total number of stars with planets containing detectable biosignatures of microbial life is expected to be highest for K-dwarfs. In contrast, we find that the corresponding value for intelligent life (technosignatures) should be highest for solar-mass stars. Thus, our work may assist in the identification of suitable targets in the search for biosignatures and technosignatures.

Liu, B., Mastalerz, M., Schieber, J., Teng, J., 2020. Association of uranium with macerals in marine black shales: Insights from the Upper Devonian New Albany Shale, Illinois Basin. International Journal of Coal Geology 217, 103351.


Marine organic-rich shales generally have high uranium content associated with sedimentary organic matter. However, organic matter in black shales is not homogeneous, but instead a mixture of different macerals. The uranium content and organic petrographic composition of 27 New Albany Shale samples indicate differential contributions of macerals to the uranium content in the Upper Devonian New Albany Shale of the Illinois Basin. Specifically, uranium is mainly associated with amorphous organic matter (microbially degraded phytoplankton, zooplankton, and bacterial biomass), where an average uranium content of approximately 550 ppm has been estimated. The amorphous organic matter's lack of structure, as well as admixed with mineral grains (<7.8 μm) suggest that it originated via microbial degradation in surficial sediments. Uranium may have been incorporated into amorphous organic matter during phytoplankton degradation and amorphous kerogen formation early in diagenesis. Pore-water redox conditions and pH control the reduction of uranium (VI) and its incorporation into amorphous organic matter. Alginite derived from Tasmanites algae (average uranium content <10 ppm) contributes minimally to uranium content. Terrestrial organic matter in the New Albany Shale contains on average ~ 20 ppm uranium, and because it accounts for <10% of total organic matter in the New Albany Shale, its contribution is equally negligible.



The origin of dolomite has long puzzled geologists. It has recently been documented that sulfate-reducing bacteria (SRB) are capable of catalyzing the formation of protodolomite, a previously proposed precursor of ordered sedimentary dolomite. However, the catalytic mechanism of SRB remains incompletely understood. This experimental study is aimed at probing the effect of capsule extracellular polymeric substances (capsule EPS) from SRB on the crystallization of protodolomite in vivo. The capsule EPS tested herein was isolated from a protodolomite-mediating SRB, Desulfotomaculum ruminis, and added into a solution wherein the degree of oversaturation was close to the growth medium of D. ruminis at stationary phase. The solid products were characterized with X-ray diffraction (XRD), Raman spectroscopy and, scanning and transmission electron microscopy (SEM and TEM). Our results indicated that aragonite emerged in the reactors without capsule EPS, while Ca-Mg carbonates (Mg-calcite and protodolomite) were produced in the systems amended with capsule EPS. The incorporation amount of Mg2+ in Ca-Mg carbonates was enhanced with the increasing concentration of capsule EPS. The predominant occurrence of protodolomite was found in the reactor with 140 mg/L capsule EPS. These resulting protodolomites were spherical in shape, and composed of numerous nano-particles. The catalytic influence of capsule EPS on the precipitation of protodolomite might be attributed to their strong Mg2+ binding capacity, potentially diminishing Mg-hydration, which is a potent inhibitor of protodolomite crystallization. The results of

Fourier transformation infrared (FT-IR) spectra showed that Mg2+ was bonded with carboxyl and hydroxyl groups on capsule EPS. This inferred adsorption capacity of capsule EPS was also supported by new calculations of complexation chemistry between Mg-H2O complex and organic compounds present in capsule EPS.



Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.



The propagation characteristic of fractures under the influence of bedding during SC-CO2 jet fracturing remains value to be studied. In order to avoid the large dispersion of natural rock property, seven types of artificial rock samples (Φ100 mm × 100 mm) with prefabricated different positions and numbers of bedding were prepared. A multifunction SC-CO2 jet system was used to conduct the SC-CO2 jet fracturing with ambient pressure. The main fractures on the surface were observed through vertical and side view after the experiment. In addition, five fracture propagation modes were summarized systematically. Finally, the fracture tortuosity parameters were obtained by quantitative analysis, and it was found that for horizontal bedding, the farther the vertical distance from the casing, the larger the fracture tortuosity formed by SC-CO2 jet fracturing; if a single fracture penetrates the bedding, the fracture tortuosity will increase.



Previous bulk sulphide analyses have suggested a correlation between the morphology of pyrite in Archean metasedimentary rocks and the sign of associated Δ33S. However, it remains to be determined whether such a correlation exists and what the underlying mechanism is. This study measured the multiple sulphur isotopic compositions of pyrite nodules and disseminated pyrite grains from two typical Neoarchean shale samples with SHRIMP-SI, following detailed textural investigations by sodium hypochlorite etching and electron microscopy. The Roy Hill Shale sample shows two generations of pyrite in both nodules and disseminated grains reflected by textures. The first generation is Δ33S-weakly negative while the second generation is Δ33S-highly positive. Both generations of pyrite show linear relationships between δ34S and Δ33S, although generation two displays wider ranges of δ34S and Δ33S compared with generation one. In the Δ33S-Δ36S diagram, generation two plots along the Archean Reference Array (ARA, Δ36S/Δ33S ≈ −1) whereas generation one deviates from the ARA in a trend similar to the Biological Fractionation Line (Δ36S/Δ33S ≈ −7). The Nammuldi shale sample also exhibits two generations of pyrite, both of which are Δ33S- and δ34S-positive albeit of different magnitude. For these two shale samples, the sign of Δ33S is not associated with the pyrite morphology. A plausible explanation for the morphology-specific Δ33S reported in previous studies could be related to bulk analyses involving pyrite of different generations with opposite Δ33S. Furthermore, based on the distribution of the earlier nodular and disseminated pyrite in both samples, a model involving four stages is proposed for the formation of pyrite nodules studied here: (1) formation of pyrite framboids composed of microcrystalline pyrite, (2) dissolution of framboidal pyrite and reprecipitation to generate larger single pyrite crystals, (3) aggregation of single pyrite crystals into nodules, and (4) injection of later hydrothermal fluids.

Liu, P., Zhan, X., Wu, X., Li, J., Wang, H., Gao, S., 2020. Effect of weathering on environmental behavior of microplastics: Properties, sorption and potential risks. Chemosphere 242, 125193.


Microplastic (MP) pollution is a raising global concern in recent years due to its wide distribution. Additionally, most of the MPs have undergone extensive weathering in the environment, and weathered MPs may exhibit different physicochemical properties from pristine ones. The review reveals the change in physicochemical properties (e.g. size, color, crystallinity, mechanical property and oxygen-containing groups) and the release of additives and MP-derived intermediates (i.e. oligomers and oxygenated compounds) during weathering processes. Weathering further affects the sorption behavior of MPs for environmental pollutants because of the changed crystallinity, specific surface area and oxygen functional groups. The interaction mechanisms of pristine and weathered MPs with pollutants are summarized, and how weathering processes affect sorption behavior is critically revealed. Because of the changed size, color and surface charges, weathered MPs might be ingested by aquatic organisms in different ways from the pristine ones. The detailed effects of weathering on the ingestion of MPs are discussed, and the potential toxicity of leachates from weathering processes is evaluated. In addition, the environmental components (e.g. natural organic matter and salinity) and biofilm correlated to the sorption behavior of MPs are reviewed. As for the knowledge gap, further studies should focus on the long-term weathering of MPs and the

relationships between weathering properties and sorption capacities toward pollutants. The potential risks of weathered MPs and leachates on organisms should be explored.

Liu, S., He, Z., Tang, Z., Liu, L., Hou, J., Li, T., Zhang, Y., Shi, Q., Giesy, J.P., Wu, F., 2020. Linking the molecular composition of autochthonous dissolved organic matter to source identification for freshwater lake ecosystems by combination of optical spectroscopy and FT-ICR-MS analysis. Science of The Total Environment 703, 134764.


Autochthonous dissolved organic matter (DOM) is increasingly released in lakes due to eutrophication, and thus affects the composition and environmental behaviors of DOM in eutrophic lakes. However, there are only limited studies on the molecular characteristics of autochthonous DOM and its influencing mechanisms. Herein, end-member DOM samples of macrophytes, algae, sediments and freshwater DOM samples in eutrophic lakes (Ch:Taihu and Dianchi) were collected and characterized by optical spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The results revealed the chemical structures of autochthonous DOM were more aliphatic and less oxidized, which was marked by increases in lipid compounds and decreases in the lignin components as compared to the allochthonous DOM-dominated freshwaters. More specially, algae-derived DOM contains more lipid (56.8%) compounds, while macrophyte-derived DOM was dominated by lignin (50.6%) and tannin (17.4%) compounds. Sediment-derived DOM contained more N-containing compounds. The traditional optical indices indicated the relative aromaticity covaried with polyphenolic and polycyclic aromatics, whereas those reflecting autochthonous DOM covaried with more aliphatic compounds. Multivariate analysis of FT-ICR-MS data of end-members and freshwaters revealed the predominant terrestrial input to Lake Taihu and greater contribution of algae released DOM to Dianchi. This study provides critical information about the characteristics of autochthonous DOM at a molecular level and confirmed autochthonous DOM was compositionally distinct from allochthonous DOM. Overall autochthonous DOM should be gained more attention in the eutrophic lakes.

Liu, X., Liu, C., Wu, J., 2019. Dynamic characteristics of offshore natural gas hydrate dissociation by depressurization in marine sediments. Geofluids 2019, 6074892.

https://doi.org/10.1155/2019/6074892

Dynamic characteristics of offshore natural gas hydrate (NGH) dissociation will provide the theoretical basis to analyze technical issues of oceanic hydrate exploitation. A mathematical model is developed to simulate offshore NGH dissociation by depressurization in marine sediments. Different phase combination statuses are involved in the process of NGH dissociation by taking ice melting and water freezing into account. The proposed methodology can analyze the processes of hydrate and water phase transitions, decomposition kinetics and thermodynamics, viscosity and permeability, ice-water phase equilibrium, and natural gas and water production. A set of an experimental system is built and consists of one 3-D visual reactor vessel, one isothermal seawater vessel, one natural gas and water separator, and one data acquisition unit. The experiments on offshore NGH dissociation by depressurization in 3-D marine sediments are carried out, and this methodology is validated against the full-scale experimental data measured. The results show that during the prophase, natural gas flow is preceded by water flow into the production wellbore and

natural gas occupies more continuous flow channels than water under a large pressure gradient. Then, the natural gas flow rate begins to decline accompanied by an increase of water production. During the second phase, natural gas flow rate decreases slowly because of the decreased temperature of hydrate-bearing formation and low pressure gradient. The lower the intrinsic permeability in marine sediments, the later the water flow rate reaches the peak production. And the space interval of the production wellbore should be enlarged by an increase of the intrinsic permeability. The stable period of natural gas production enhances, and the water flow rate reduces with the increase of bottom-hole pressure in production wellbores. The main reason is the slow offshore NGH dissociation under the low producing pressure and the restriction of heat conductivity under the low temperature.

Liu, Y., Chen, C., He, D., Chen, W., 2019. Deep carbon cycle in subduction zones. Science China Earth Sciences 62, 1764-1782.

https://doi.org/10.1007/s11430-018-9426-1

The carbon cycle between the deep Earth and the atmosphere (i.e., the deep carbon cycle) can significantly affect the global climate on both long and short time scales. Although carbon in the deep Earth can be released to the atmosphere in many ways, plate subduction is the only pathway for the return of carbon from the surface to the deep Earth. Owing to diversity in the forms of carbon and the special physicochemical property of carbonates, the behavior of carbon and carbonates in subduction zones significantly affects the products of subduction processes, the oxygen fugacity in subduction zones, and the activation and migration of elements during the crust-mantle interaction. Therefore, the carbon cycle in subduction zones plays an important role in maintaining a habitable climate by regulating the atmospheric CO2 concentration, which significantly affects the global climate, and in causing fundamental changes in the physical and chemical properties of the mantle that result in a heterogeneous mantle. In this study, we review and discuss previous studies and scientific problems regarding the carbon cycle in subduction zones from four aspects: observation and tracing of the carbon cycle, migration and variation of carbon during subduction, carbon flux, and the effect of the carbon cycle.

Liu, Y., Ma, W., Kou, D., Niu, X., Wang, T., Chen, Y., Chen, D., Zhu, X., Zhao, M., Hao, B., Zhang, J., Yang, Y., Hu, H., 2019. How deep do we dig for surface soil? A comparison of patterns of microbial C:N:P stoichiometry between topsoil and subsoil along an aridity gradient. Biogeosciences Discussions 2019, 1-36.


Microbial stoichiometry and its driving factors play crucial roles in understanding the balance of chemical elements in ecological interactions and nutrient limitations along aridity gradients. However, little is known about the variation in these features along aridity gradients due to the lack of comprehensive field investigations. Additionally, previous studies focused on the surface soil (0–10 or 0–20 cm); however, the minimum sampling depth for surface soil could impact the results of the vertical distribution of microbial stoichiometry. In the present study, we measured the variation in microbial stoichiometry, examined the major influential factors (climatic, edaphic and biotic factors) along an aridity gradient and determined whether the sampling depth affected microbial C : N : P stoichiometry. We found that the microbial C : N (topsoil: 6.59; subsoil: 6.83), C : P (topsoil:

60.2; subsoil: 60.5) and N : P ratios (topsoil: 9.29; subsoil: 8.91) varied with soil depth and that the microbial C : N ratio significantly increased with soil depth. The microbial C : N ratio significantly increased with increasing aridity for both topsoil and subsoil, while the microbial N : P ratio decreased along the aridity gradient only for the topsoil), which implied that drought-stimulated microbes tend to be more N conservative, especially for the topsoil. Among all the factors, the soil organic carbon (SOC) content and fungi to bacteria ratio exerted the largest influence on the microbial C : N, C : P and N : P ratios at both soil depths, implying that the substrate supply and microbial structure together controlled the microbial stoichiometry. The results also revealed that the aridity index (AI) and plant aboveground biomass (AGB) influenced the C : N ratio in microbial biomass at both soil depths, and the effects of those factors decreased in the subsoil. The results of this study suggested that the flexibility of the microbial N : P ratio should be considered when establishing the minimum sampling depth in a vertical study. The present study also represented the first attempt to examine the patterns of soil microbial stoichiometry for different soil depth along an aridity gradient.

Liu, Z., Chen, D., Zhang, J., Lv, X., Dang, W., Liu, Y., Liao, W., Li, J., Wang, Z., Wang, F., 2019. Combining isotopic geochemical data and logging data to predict the range of the total gas content in shale: A case study from the Wufeng and Longmaxi shales in the Middle Yangtze area, South China. Energy & Fuels 33, 10487-10498.


The marine shales of the lower Silurian Longmaxi formation (S1l) and the upper Ordovician Wufeng formation (O3w) in the middle Yangtze area of southern China have been recognized as effective gas shales with an enormous potential. To estimate the total gas content in the shales, shale gas samples were collected at 20 °C, 48 °C/65 °C, and 90 °C in the gas release process of each core sample during desorption experiments. Based on the isotope fractionation data during the desorption of gas in shale, an adsorbed gas content(mixture gas)/free gas content(mixture gas) to δ13C1(mixture gas) model was established to estimate the proportions of free and adsorbed gas in shale by using the δ13C1 data of shale gas. The proportion of adsorbed gas(mixture gas) in the Wufeng shales is higher than that in the Longmaxi gas shales. The adsorption capacity of the Wufeng shales with relatively high total organic carbon (TOC) is greater than that of the Longmaxi shales with a relatively low TOC. Subsequently, the free gas content and the adsorbed gas content could be calculated during the desorption experiments. Combining the free gas and adsorbed gas estimated from the logging data, we calculated the minimum and maximum total gas contents of each core sample from well LY1. The total gas content in the Wufeng shales, ranging from 1.654 to 3.371 m3/t, is higher than that of the Longmaxi shales, ranging from 0.398 to 1.769 m3/t. Compared with the minimum and maximum total gas contents predicted by the isotopic geochemical data and logging data, the value of the total gas content estimated by using the United States Bureau of Mines method is not always located within the range of the total gas content, which is influenced by the relationship between free gas(logging data) (m3/t) and free gas(measured gas) (m3/t).

Liu, Z., Zhang, F., Li, X., 2019. Elastic anisotropy and its influencing factors in organic-rich marine shale of southern China. Science China Earth Sciences 62, 1805-1818.

https://doi.org/10.1007/s11430-019-9449-7

Shale is observed to have strong anisotropy due to its unique mineralogy and microstructure, and this anisotropy property has significant impact on seismic and well-log data. The organic-rich marine shale in the southern and eastern Sichuan Basin is one of the most important shale-gas reservoir formations in China. To investigate the elastic anisotropy of this shale and its influencing factors, we performed ultrasonic velocity measurements, X-ray diffraction analysis, rock-eval pyrolysis and vitrinite reflectance measurement on the samples from the Upper Ordovician Wufeng Formation and the Lower Silurian Longmaxi Formation. The experimental results show the that: (1) the velocity anisotropy of the Wufeng-Longmaxi (WL) shale varies from 10% to 50%, and most samples have strong anisotropy; (2) the P- and S-wave anisotropy parameters (Thomsen’s ε and γ) increase with clay contents, but this relationship can be greatly affected by the clay orientation index; (3) organic matter content (OMC) is found to have little influence in seismic anisotropy for the over mature WL shale, whereas the OMC determines the magnitude of anisotropy of immature/mature shales (e.g. the Bakken shale or the Bazhenov shale) according to the published literatures, because organic matters in shales of different maturity have different morphologies and distributions; (4) the OMC of WL shale has positive correlation with quartz content, and this weakens the correlation between OMC and the magnitude of anisotropy to a certain extent. The results of this study provide an important rock-physics basis and data support for seismic anisotropy exploration, quantitative interpretation and resource evaluation of the organic-rich marine shales in southern China.

Lombardi, F., Lodi, A., Ma, J., Liu, J., Slota, M., Narita, A., Myers, W.K., Müllen, K., Feng, X., Bogani, L., 2019. Quantum units from the topological engineering of molecular graphenoids. Science 366, 1107-1110.


Abstract: Robustly coherent spin centers that can be integrated into devices are a key ingredient of quantum technologies. Vacancies in semiconductors are excellent candidates, and theory predicts that defects in conjugated carbon materials should also display long coherence times. However, the quantum performance of carbon nanostructures has remained stunted by an inability to alter the sp2-carbon lattice with atomic precision. Here, we demonstrate that topological tailoring leads to superior quantum performance in molecular graphene nanostructures. We unravel the decoherence mechanisms, quantify nuclear and environmental effects, and observe spin-coherence times that outclass most nanomaterials. These results validate long-standing assumptions on the coherent behavior of topological defects in graphene and open up the possibility of introducing controlled quantum-coherent centers in the upcoming generation of carbon-based optoelectronic, electronic, and bioactive systems.

Editor's Summary: Controlling quantum defects in graphene. The development of quantum technologies relies on the ability to fabricate and engineer materials with robust quantum properties. The controlled introduction of defects in semiconductors is one of the most promising platforms under development. With the capability to precisely position point defects (five-membered rings) in the graphene honeycomb lattice, Lombardi et al. explored recent theoretical work suggesting that such defects should display enhanced quantum properties (see the Perspective by von Kugelgen and Freedman). The spin-bearing properties of the defects and the engineered control of their interactions open up exciting possibilities for graphene-based spintronics and quantum electronics.

Losch, A., 2019. Planetary sustainability: transitions of an idea. International Journal of Astrobiology 18, 592-594.

https://doi.org/10.1017/S147355041900003X

Comment on: Beisbart, C (2019) Is trans-planetary sustainability a good idea? – An answer from the perspective of conceptual engineering. International Journal of Astrobiology. https://doi.org/10.1017/S1473550418000472

Reply to Comment: Beisbart, C., 2019. (Trans-)planetary sustainability once more – a reply to Losch. International Journal of Astrobiology 18, 590-591.

Lowenthal, M.S., Quittman, E., Phinney, K.W., 2019. Absolute quantification of RNA or DNA using acid hydrolysis and mass spectrometry. Analytical Chemistry 91, 14569-14576.


Accurate, traceable quantification of ribonucleotide or deoxyribonucleotide oligomers is achievable using acid hydrolysis and isotope dilution mass spectrometry (ID-MS). In this work, formic acid hydrolysis is demonstrated to generate stoichiometric release of nucleobases from intact oligonucleotides, which then can be measured by ID-MS, facilitating true and precise absolute quantification of RNA, short linearized DNA, or genomic DNA. Surrogate nucleobases are quantified with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow, using multiple reaction monitoring (MRM). Nucleobases were chromatographically resolved using a novel cation-exchange separation, incorporating a pH gradient. Trueness of this quantitative assay is estimated from agreement among the surrogate nucleobases and by comparison to concentrations provided for commercial materials or Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST). Comparable concentration estimates using NanoDrop spectrophotometry or established from droplet-digital polymerase chain reaction (ddPCR) techniques agree well with the results. Acid hydrolysis-ID-LC-MS/MS provides excellent quantitative selectivity and accuracy while enabling traceability to mass unit. Additionally, this approach can be uniquely useful for quantifying modified nucleobases or mixtures.

Lu, J., Zhu, M., 2019. The postparietal shield of the Pragian dipnomorph Arquatichthys and its implications for the rhipidistian cranial anatomy. Palaeoworld 28, 543-549.


Rhipidistians comprise dipnomorphs (the lungfish lineage) and tetrapodomorphs (the tetrapod lineage). Arquatichthys porosus Lu and Zhu, 2008 is a Pragian dipnomorph from the Posongchong Formation of Zhaotong, Yunnan, South China (∼409 million years ago, Early Devonian), previously represented by a lower jaw and few scattered scales. Here we describe a newly-discovered postparietal shield of Arquatichthys by means of high-resolution computed tomography. The cranial morphology of Arquatichthys resembles that of the basal dipnomorph Powichthys in having more than two supratemporal bones each side, more than one row of openings for sensory canals on the marginal bones, and a straight posterior margin of the shield. An intricate occipital artery system is present between the skull roof and neurocranium, as in Youngolepis and the tetrapodomorph Eusthenopteron. The discovery of the postparietal shield of Arquatichthys adds new evidence in the

cranial evolution of rhipidistians, and helps to improve our understanding of the character transformations during the early diversification of rhipidistians.

Lu, K., Liu, Z., 2019. Molecular level analysis reveals changes in chemical composition of dissolved organic matter from South Texas rivers after high flow events. Frontiers in Marine Science 6, 673. doi: 10.3389/fmars.2019.00673.


Riverine dissolved organic matter (DOM) is a major source of reduced carbon exported from land to marine environments, and the inflow of riverine organic matter greatly affects biogeochemical cycling in estuaries and bays. Thus, any change in DOM composition, such as changes caused by flood waters as a result of storms and hurricanes, can subsequently affect estuarine environments. To investigate the impact of high flow events on riverine DOM, multidimensional molecular level information on DOM from four South Texas Rivers (Aransas, Lavaca, Mission, and Nueces Rivers) was acquired using high-resolution Ion Mobility Quadrupole Time of Flight Liquid Chromatography Mass Spectrometry (IM Q-TOF LCMS). Base-flow samples were collected in May, July, and October of 2016, June of 2017, and March of 2018, while high-flow samples were collected in September of 2017, as well as June and September of 2018. Based on the molecular formulas assigned from IM Q-TOF LCMS, the H/C ratio decreased during high-flow events (1.52 to 1.51 in ESI+ and 1.19 to 1.07 in ESI−), while the O/C ratio increased (0.31 to 0.33 in ESI−). Furthermore, DOM shifted from a protein-like and lipid-like dominated community at base flow conditions, to a lignin, tannin and condensed aromatic structure dominated community during high flow events, based on MS and tandem MS data. These changes in high-flow riverine DOM indicate an increase of terrestrial signal, which is likely a result of mobilization of terrestrial organic matter from the watersheds by flooding. The mobilized DOM, though refractory at high-flow conditions in rivers, could be reactive in coastal regions when conditions change, and thus could potentially fuel microbial activities downstream. In addition, about 3.76–21.8% of DOM molecules contain structural isomers among different flow conditions. This low number of isomer percentages suggests that DOM, as the products of various enzymatic biochemical reactions, is constrained in the number of isomers. Taken together, results from our study provide insights into structural changes of riverine DOM in response to extreme climate events in subtropical regions and have implications in understanding biogeochemical changes in estuaries under a changing climate.

Lüning, S., Schulte, L., Garcés-Pastor, S., Danladi, I.B., Gałka, M., 2019. The Medieval Climate Anomaly in the Mediterranean region. Paleoceanography and Paleoclimatology 34, 1625-1649.

https://doi.org/10.1029/2019PA003734

Abstract: The Medieval Climate Anomaly (MCA) is a preindustrial phase of pronounced natural climate variability with a core period from 1000 to 1200 CE. The paper presents a synthesis that integrates palaeotemperature records from the Greater Mediterranean Region encompassing the past 1,500 years based on multiproxy data from 79 published land and marine sites. MCA warming dominated the Western Mediterranean (Iberia, NW Africa) as well as the northern land areas of the Central and Eastern Mediterranean region. MCA cooling prevailed in the Canary Current Upwelling System, southern Levant, and some sea areas of the Central and Eastern Mediterranean. Previous palaeoreconstructions suggest persistent positive Atlantic Multidecadal Oscillation (AMO+) and

North Atlantic Oscillation (NAO+) conditions during the MCA, while the Little Ice Age was dominated by an AMO− and NAO− regime. During the past 150 years, AMO+ conditions are typically associated with warming episodes in the Mediterranean area. A similar relationship appears to have also been established during the MCA as the majority of all Mediterranean land sites experienced warm climate conditions. In contrast, the NAO typically leads to a characteristic west east temperature ‐dipole pattern in the basin, as documented for the last decades. During NAO+ conditions the Western Mediterranean is generally warm (and dry), while large parts of the Central and Eastern Mediterranean are cold. Similar trends seem to have been developed during the MCA when the NAO+ regime led to consistent warming in the Western Mediterranean, while a significant number of sites with MCA cooling existed in the Central and Eastern Mediterranean.

Plain Language Summary: Mediterranean climate has been warming significantly over the past 100 years with anthropogenic climate change having become a key issue. In order to better understand modern climatic change, developments need to be placed into a longer term preindustrial context ‐to compare with times when human CO2 emissions did not yet play a major role for climate. This paper integrates data on Medieval temperature trends from 79 published Mediterranean land and marine sites. Our synthesis shows that the Western Mediterranean (Iberia, Northwest Africa) as well as the northern land areas of the Central and Eastern Mediterranean region have experienced a warm phase 1000–1200 CE, corresponding to the so called “Medieval Climate Anomaly.” ‐Contemporaneous cooling occurred in other parts of the Greater Mediterranean region, namely, in the southern Levant, some sea areas of the Central and Eastern Mediterranean, and the Canary Current Upwelling System. The regional differences in Medieval Mediterranean temperature trends show a pattern, which partly resembles modern multidecadal temperature variability in the area. The main drivers of these patterns appear to be Atlantic ocean cycles (AMO, NAO), which episodically shift between positive and negative phases and lead to characteristic temperature effects in the region.

Luo, Q., Fariborz, G., Zhong, N., Wang, Y., Qiu, N., Skovsted, C.B., Suchý, V., Hemmingsen Schovsbo, N., Morga, R., Xu, Y., Hao, J., Liu, A., Wu, J., Cao, W., Min, X., Wu, J., 2020. Graptolites as fossil geo-thermometers and source material of hydrocarbons: An overview of four decades of progress. Earth-Science Reviews 200, 103000.


The thermal maturity of lower Paleozoic graptolite-bearing marine sediments, which host many hydrocarbon deposits worldwide, has long been difficult to determine due to the absence of wood-derived vitrinite particles for conventional vitrinite reflectance. In 1976, graptolite reflectance was introduced as a new indicator for organic maturity of these deposits and has been used since in many regional studies. The majority of these studies, however, were done on a limited sample set and a limited range of thermal maturity, which resulted in a number of controversial views concerning the usefulness of graptolite reflectance as an alternative paleothermal indicator and its correlation with vitrinite reflectance through various proxies. In this paper, we review previous studies and combine those analyses with new data to assess the physical and chemical characteristics of graptolite periderm with increasing thermal maturity. We conclude that graptolite random reflectance (GRor) is a better parameter for the thermal maturity assessment than graptolite maximum reflectance (GRomax) due to the better quality of available data. Combining published data with results of our study of both natural and heat-treated graptolites and vitrinite, we present a new correlation between GRor and equivalent vitrinite reflectance (EqVRo), as EqVRo = 0.99GRor + 0.08.

Chemical composition of graptolite periderm is similar to vitrinite; graptolites are mainly kerogen Type II-III, are gas prone and have a substantial hydrocarbon potential. Lower Paleozoic graptolite-bearing organic-rich sediments are important shale gas source rocks and reservoirs globally and make a significant contribution to worldwide petroleum reserves.

Luong, S., Tocheri, M.W., Hayes, E., Sutikna, T., Fullagar, R., Saptomo, E.W., Jatmiko, Roberts, R.G., 2019. Combined organic biomarker and use-wear analyses of stone artefacts from Liang Bua, Flores, Indonesia. Scientific Reports 9, 17553.

https://doi.org/10.1038/s41598-019-53782-2

Organic biomarker and lithic use-wear analyses of archaeological implements manufactured and/or used by hominins in the past offers a means of assessing how prehistoric peoples utilised natural resources. Currently, most studies focus on one of these techniques, rather than using both in sequence. This study aims to assess the potential of combining both methods to analyse stone artefacts, using a set of 69 stones excavated from the cave site of Liang Bua (Flores, Indonesia). Prior to chemical analysis, an initial inspection of the artefacts revealed potential use-wear traces but no visible residues. Gas chromatography mass spectrometry (GC-MS) analysis, including the targeting of 86 lipids, terpenes, terpenoids, alkanes and their analogues, found compounds with plant or animal origin on 27 of the 69 stones. The artefacts were subsequently cleaned, and use-wear analysis identified traces of use on 43 artefacts. Use-wear analysis confirmed traces of use on 23 of the 27 artefacts with potential use-residues that were determined by GC-MS. The GC-MS results were broadly consistent with the functional classes identified in the later use-wear analysis. This inclusive approach for stone artefact analysis strengthens the identifications made through multiple lines of enquiry. There remain conflicts and uncertainties in specific cases, suggesting the need for further refinement and analyses of the relationships between use-wear and residues.

Luque, J., Gerken, S., 2019. Exceptional preservation of comma shrimp from a mid-Cretaceous Lagerstätte of Colombia, and the origins of crown Cumacea. Proceedings of the Royal Society B: Biological Sciences 286, 20191863.


Mesozoic rocks with exceptional preservation of marine arthropods are known worldwide but largely restricted to mid–high latitudes. The scarcity of assemblages with exceptional preservation in low, tropical latitudes greatly limits our understanding of the origins of several modern groups and the evolution of tropical biotas through time. Here, we report the oldest crown Cumacea, or ‘comma’ shrimp (Arthropoda: Eumalacostraca: Peracarida) with modern familial affinities, from a new mid-Cretaceous (95–90 Ma) Lagerstätte in tropical South America. Cumaceans have one of the poorest fossil records among marine arthropods, despite today being abundant and speciose benthic organisms associated with fine-grained sediments with high fossilization potential. Eobodotria muisca gen. et sp. nov., found in mass accumulation surfaces, preserves with detail the gut, mouth parts, thoracic legs/pereopods, pleopods, uropods bearing setae, antennal flagella and even small eyes bearing ommatidia. These features, rarely preserved in fossil crustaceans, plus the large sample size (greater than 200 individuals, 6–8 mm long), allow us to discuss phylogenetic/systematic aspects and explore possible mechanisms behind their unusual accumulation. Eobodotria bridges an approximately 165 Myr gap in the cumacean fossil record,

provides a reliable calibration point for phylogenetic studies and expands our understanding of exceptional preservation in past and present tropical settings.



Paleogene Huangxian Basin which lies in Eastern China contains deposits of many types of coal and shale associations. The sedimentary models of coal and shale associations are very important to explore the coal and shales. However, whether the transgression affected the lithofacies and geochemical characteristics of coal and shale in the Paleogene Huangxian Basin in eastern China has not been reported in detail, which is important to construct the sedimentary models. In this study, petrological and geochemical methods are used to comprehensively analyze the mineral composition, contents of major and trace elements, and distribution characteristics of geochemical parameters of coal and shale in Huangxian Basin. The results show that coal and shale have different macerals. The study of typical geochemical parameters (Mn/Ti, K2O/Na2O, Sr/Ba, and Th/U) shows that the no. 1 coal seam (CB1) and no. 4 coal seam (CB4) are least affected by seawater, while the no. 1-3 coal seam (CB1-3) is affected by seawater to some extent. Shale 1-3 (S1-3), shale 2 (S2), and shale 4 (S4) are affected by seawater, while shale 1 (S1) is little affected by seawater. In order to discuss the sedimentary model of coal and shale, the tectonic background, provenance, paleoclimate, and fault movement of Huangxian basin are analyzed. The results show that the basin is located at the continental island arc and the active continental margin. Transgression and tectonic movement affect the input of terrigenous debris. The paleoclimate during coal formation was warmer and wetter, while shale was cooler and drier. During basin subsidence, CB4–S4 and CB1–S2–S1 combinations were basically formed under the influence of transgression driven by paleoclimate change. The combination of S1-3 and CB1-3 was formed in a stable freshwater lacustrine environment, followed by transgression.

Lv, J., Liu, F., Han, W., Wang, Y., Zhu, Q., Zang, J., Wang, S., Zhang, B., Wang, N., 2019. The effect of nitrogen content on archaeal diversity in an Arctic lake region. Microorganisms 7, 10.3390/microorganisms7110543.


The function of Arctic soil ecosystems is crucially important for the global climate, and nitrogen (N) is the major limiting nutrient in these environments. This study assessed the effects of changes in nitrogen content on archaeal community diversity and composition in the Arctic lake area (London Island, Svalbard). A total of 16S rRNA genes were sequenced to investigate archaeal community composition. First, the soil samples and sediment samples were significantly different for the geochemical properties and archaeal community composition. Thaumarchaeota was an abundant phylum in the nine soil samples. Moreover, Euryarchaeota, Woesearchaeota, and Bathyarchaeota were significantly abundant phyla in the three sediment samples. Second, it was found that the surface runoff caused by the thawing of frozen soil and snow changed the geochemical properties of soils. Then, changes in geochemical properties affected the archaeal community composition in the soils. Moreover, a distance-based redundancy analysis revealed that NH4

+–N (p < 0.05) and water

content were the most significant factors that correlated with the archaeal community composition. Our study suggests that nitrogen content plays an important role in soil archaeal communities. Moreover, archaea play an important role in the carbon and nitrogen cycle in the Arctic lake area.

Lv, W., Shi, X., Wang, S., Xu, G., 2019. Multidimensional liquid chromatography-mass spectrometry for metabolomic and lipidomic analyses. TrAC Trends in Analytical Chemistry 120, 115302.


As important components of omics, metabolomics and lipidomics are dedicated to detecting as many metabolites and lipids as possible, respectively, in biological samples. Because the physicochemical properties of metabolites and lipids greatly differ, the comprehensive analysis of metabolomics and lipidomics using one dimensional liquid chromatography-mass spectrometry is extremely difficult. Benefited from the combination of different separation mechanisms, multidimensional liquid chromatography (MDLC) has been considered a powerful approach for the analysis of complex samples. In this review, the construction modes and modulation modes of MDLC and its applications mainly in last five years in the field of metabolomic and lipidomic analyses are summarized in details. In addition to common interfaces (i.e., heart-cutting, stop-flow and comprehensive mode with a storage loop and trap column), the novel construction modes (i.e., selective comprehensive and pulsed-elution 2DLC, stop-flow 3DLC) and modulation modes (e.g., vacuum evaporation interface and evaporation membrane modulation etc.) are also introduced.

Lyson, T.R., Miller, I.M., Bercovici, A.D., Weissenburger, K., Fuentes, A.J., Clyde, W.C., Hagadorn, J.W., Butrim, M.J., Johnson, K.R., Fleming, R.F., Barclay, R.S., Maccracken, S.A., Lloyd, B., Wilson, G.P., Krause, D.W., Chester, S.G.B., 2019. Exceptional continental record of biotic recovery after the Cretaceous–Paleogene mass extinction. Science 366, 977.


Abstract. We report a time-calibrated stratigraphic section in Colorado that contains unusually complete fossils of mammals, reptiles, and plants and elucidates the drivers and tempo of biotic recovery during the poorly known first million years after the Cretaceous–Paleogene mass extinction (KPgE). Within ~100 thousand years (ka) post-KPgE, mammalian taxonomic richness doubled, and maximum mammalian body mass increased to near pre-KPgE levels. A threefold increase in maximum mammalian body mass and dietary niche specialization occurred at ~300 ka post-KPgE, concomitant with increased megafloral standing species richness. The appearance of additional large mammals occurred by ~700 ka post-KPgE, coincident with the first appearance of Leguminosae (the bean family). These concurrent plant and mammal originations and body-mass shifts coincide with warming intervals, suggesting that climate influenced post-KPgE biotic recovery.

Editor's summary. Terrestrial record of recovery: The extinction that occurred at the end of the Cretaceous period is best known as the end of the nonavian dinosaurs. In theory, this paved the way for the expansion of mammals as well as other taxa, including plants. However, there are very few direct records of loss and recovery of biotic diversity across this event. Lyson et al. describe a new record from the Cretaceous-Paleogene in Colorado that includes unusually complete vertebrate and plant fossils that describe this event in detail, including the recovery and expansion of mammalian body size and increasing plant and animal biotic diversity within the first million years.

Ma, X., Huang, C., Shi, Y., 2019. Oil and gas enrichment patterns and major controlling factors for stable and high production of tight lacustrine carbonate rocks, a case study of Yingxi area in Qaidam Basin, West China. Carbonates and Evaporites 34, 1815-1831.

https://doi.org/10.1007/s13146-019-00529-9

In recent years, sustained important discoveries of oil and gas exploration in the E32 reservoir of

Oligocene in the Yingxi area have been achieved, which revealed great exploration potential in Qaidam Basin. Based on core observations and systematic research on micro-petrological and structural characteristics, lithology, hydrocarbons enrichment patterns, and major controlling factors of stable and high production of the Oligocene reservoir in the Yingxi area of Qaidam were studied. The following findings were reported: (1) the lithology of the target layer is mainly lacustrine carbonate rocks, which can be divided into inter-salt and subsalt strata. In addition, many thick layers of halites widely developed in inter-salt strata. While thin layers of gypsum also developed scatteringly in the subsalt strata. (2) Fine-grained lacustrine carbonate rocks (including dark mudstone) were deposited under saline conditions, which not only are relatively the best quality source rock, but also developed a “dessert” dolomite reservoir. This set of strata is characteristic of “authigenic source rock and authigenic reservoir”. The upper salt layers have a strong sealing ability because of their very high capillary breakthrough pressure and plastic characteristics, and joints formed widely in the subsalt strata since stress concentration. The good matching relationship among all of the above factors led to the formation of favorable area for large-scale hydrocarbon accumulation in the subsalt strata. (3) The development of the matrix intercrystalline pores controls the scale of oil and gas reservoirs and stable production. Moreover, the development of fractures controls the enrichment of oil and gas reservoirs and high production. The research results have important guiding significance for further research on subsalt oil and gas distributing regularities, as well as further exploration deployment of E3

2 in the Yingxi area.

Ma, X., Huang, C., Shi, Y., Chang, H., Zhao, F., 2019. Unique hydrocarbon-generating mechanism of Oligocene evaporites of Qaidam Basin, West China. Carbonates and Evaporites 34, 1455-1467.

https://doi.org/10.1007/s13146-019-00484-5

The principle hydrocarbon source in West Qaidam Basin, China, is the Xiaganchaigou formation, which charges a series of Cenozoic large reservoirs. We identified a series of organic-rich intervals within a sequence of Oligocene-age Xiaganchaigou evaporites in southwest Qaidam. By analyzing 2D and 3D seismic tomography and gamma ray well logs, we defined the distribution and extent of these source rocks. We also characterized their composition with trace element analysis and carbon and oxygen isotope measurements. Our data demonstrated distinctive characteristics of these source rocks with high salinity, abundant organic material, high hydrocarbon generation efficiency, and low maturity, which are associated with relatively rapid and productive hydrocarbon generation. Using high-pressure and high temperature experiments to simulate pyrolysis in samples of the source rocks, we investigated what enabled these young salt-rich source rocks to generate such an abundance of hydrocarbons. Our results highlighted the key role of saline and radioactive minerals in catalyzing accelerated pyrolysis of hydrocarbons during diagenesis and catagenesis. Salt catalysis clearly played an important role in hydrocarbon generation within lower maturity

formations and also significantly improved and redefined the source rocks distribution and the extent of probable reserves in the southwest Qaidam.



Shale gas reservoir performance and canister desorption experiments of the Lower Cambrian organic-rich shales in the eastern Upper Yangtze Platform reveal a significant difference in shale gas content between the Dabashan arc-like fold-thrust belt in northeastern Chongqing (Deformed Zone) and the slightly folded area in southeastern Chong (Non-deformed Zone). Integrated pore characterization methods including scanning electron microscopy (SEM), low-temperature N2 and CO2 adsorption, and mercury injection capillary pressure (MICP) analyses were comparatively conducted in both areas in order to examine shale gas reservoir pore size variations and thus the possible microscopic pore structure controls on shale gas enrichment.

The Lower Cambrian shales in both Deformed Zone (DZ) and Non-deformed Zone (NDZ) were deposited in the deep-water shelf and show similar organic matter richness and thermal maturity. The majority of organic matter (OM)-hosted pores in DZ samples are in nanoscale size range with the dominance of micro-fractures within the OM or at the interface of OM and minerals. In contrast, OM-hosted meso-(2–50 nm) to macropores (>50 nm) are the dominant pore types in the NDZ samples. OM-hosted micropores (<2 nm) are abundant in both zones. Helium ion microscopy observations further confirm the presence of OM-hosted micropores in the studied samples. Mineral-hosted pores in carbonate minerals are abundant in both zones, while dissolution rims around carbonate minerals are more abundant in NDZ samples.

The Dabashan arc-like fold-thrust belt took place by the end of the Late Triassic, while the Lower Cambrian shales have reached thermal maturity peak. OM-hosted meso-(2–50 nm) to macropores (>50 nm) in DZ samples are most probably collapsed during structural deformation related to tectonic compression, while micropores due to their smaller size survived the tectonic stress. The OM-hosted micropores are the main storage space for adsorbed gas in the DZ area. The dominance of micro-pores in DZ and lack of connection between those pores and matrix pores led to higher gas content in DZ samples. On the contrary, the well-connected OM-hosted pore network in NDZ allows easier gas flow in the rock matrix that eventually led to significant gas leakage during uplift and exhumation and lower gas content in this zone. The results of this study suggest that structural deformation can potentially change the pore structure of shales and thus shale gas content which has major significance for shale gas exploration and development in south China where had experienced complex tectonic movements.



Four shale samples from the Lower Silurian Longmaxi Formation and the Lower Cambrian Shuijingtuo Formation in the eastern part of Chongqing, SW China, were subjected to canister desorption experiments at reservoir and elevated temperatures (up to 90 °C) to investigate shale gas release behaviors and their variations in chemical and isotopic compositions of desorbed gases. Both the ratios of gas released at reservoir temperature to the total desorbed gas at reservoir and elevated temperatures and the desorption rates suggest that the Longmaxi shale gas is more easily released than the Shuijingtuo shale gas. Scanning electron microscope (SEM) observation, along with low temperature CO2 and N2 adsorption results, suggests that organic matter hosted pores with diameters of 2–100 nm are rich in the Longmaxi shales, whereas well-developed micropores (<2 nm) are characteristics of the organic matter in the Shuijingtuo shales. High proportions of organic matter hosted micropores and high TOC contents, coupled with a poorly connected organic matter hosted pore network, result in the dominance of adsorbed gas in the Shuijingtuo shales and subsequent difficulty for gas release. Both the CO2/CH4 and C2H6/CH4 ratios of the incrementally collected desorbed gas, increase with the extent of desorption, whereas the C2H6/CH4 ratio increases first and then decreases after a peak. The changes in chemical composition of desorbed gas with desorption process are mainly caused by both the difference of adsorption capacity of shales and the varying molecular sizes of CH4, C2H6 and CO2. Carbon isotopic values of incrementally collected desorbed methane become rapidly 13C-enriched as desorption proceeds at reservoir temperatures, and up to 13.7–16.2‰ and 9.1–10.2‰ for the Longmaxi and Shuijingtuo shales respectively. At elevated temperatures (60 and 90 °C), a similar trend was observed but the desorbed gas is initially 13C-depleted. Isotopic fractionation and mass balance calculations of lost gas and desorbed gas suggest that the in situ δ13CCH4 values of shale gas were approximately represented by the δ13CCH4 values of desorbed gas collected at the 5th hour of canister desorption at reservoir temperature. This corresponds typically to a stage when 42–70% of potentially available gas is released from the shale. Thus shale gas content and gas chemistry data from canister desorption of freshly obtained core samples provides valuable geochemical information for understanding shale gas production behavior in the field.

MacDonald, B.L., Stalla, D., He, X., Rahemtulla, F., Emerson, D., Dube, P.A., Maschmann, M.R., Klesner, C.E., White, T.A., 2019. Hunter-gatherers harvested and heated microbial biogenic iron oxides to produce rock art pigment. Scientific Reports 9, 17070.

https://doi.org/10.1038/s41598-019-53564-w

Red mineral pigment use is recognized as a fundamental component of a series of traits associated with human evolutionary development, social interaction, and behavioral complexity. Iron-enriched mineral deposits have been collected and prepared as pigment for use in rock art, personal adornment, and mortuary practices for millennia, yet little is known about early developments in mineral processing techniques in North America. Microanalysis of rock art pigments from the North American Pacific Northwest reveals a sophisticated use of iron oxide produced by the biomineralizing bacterium Leptothrix ochracea; a keystone species of chemolithotroph recognized in recent advances in the development of thermostable, colorfast biomaterial pigments. Here we show evidence for human engagement with this bacterium, including nanostructural and magnetic properties evident of thermal enhancement, indicating that controlled use of pyrotechnology was a key feature of how biogenic iron oxides were prepared into paint. Our results demonstrate that hunter-gatherers in this area of study prepared pigments by harvesting aquatic microbial iron mats dominated by iron-oxidizing bacteria, which were subsequently heated in large open hearths at a

controlled range of 750 °C to 850 °C. This technical gesture was performed to enhance color properties, and increase colorfastness and resistance to degradation. This skilled production of highly thermostable and long-lasting rock art paint represents a specialized technological innovation. Our results contribute to a growing body of knowledge on historical-ecological resource use practices in the Pacific Northwest during the Late Holocene.

Maceira, A., Marcé, R.M., Borrull, F., 2020. Analytical methods for determining organic compounds present in the particulate matter from outdoor air. TrAC Trends in Analytical Chemistry 122, 115707.


Different analytical techniques can be used to chemically characterize the atmospheric particulate matter, and to provide information about the concentration range, sources, fates and distributions of different atmospheric pollutants. This review describes the available and currently most-used analytical methods for PM characterization. Although it is not an exhaustive study about the whole characterization of the air PM, some particular case studies are presented. Most of the methods described are mainly based on gas chromatography, although techniques such as liquid chromatography or others, such as Fourier transform infrared spectroscopy, are also presented. Moreover, sample pre-treatments, extraction and clean-up techniques and the mentioned determination techniques are described and discussed, showing their main features as well as their advantages and drawbacks. Therefore, this review could be a useful guide for readers to choose the most suitable techniques for their purposes since it reports different advances in PM characterization during the last decade.

Macquet, M., Lawton, D.C., Saeedfar, A., Osadetz, K.G., 2019. A feasibility study for detection thresholds of CO2 at shallow depths at the CaMI Field Research Station, Newell County, Alberta, Canada. Petroleum Geoscience 25, 509.

http://pg.lyellcollection.org/content/25/4/509.abstract

We present the results of a feasibility study for seismic monitoring using conventional surface seismic experiments at the CaMI Field Research Station, Alberta, Canada, where a small volume of gas-phase CO2 is being injected into a sandstone reservoir at a depth of 300 m. We first apply a careful fluid substitution procedure to the results of reservoir gas saturation and pressure responses obtained from fluid flow simulations. We test different methods to compute the bulk modulus of the fluid for different fluid saturation models. Assuming a semi-patchy model and considering only the replacement of brine with a maximum saturation of 50% CO2, we estimate the reduction in P-wave velocity to be 20%. Adding an increase in pore pressure of 2.7 MPa increases the P-wave velocity reduction to 32%. After including a field-based signal-to-noise ratio of 5% to the synthetic seismic data, the time-lapse seismic anomaly should be detectable after one year of injection (266 tonnes of CO2).

Maier, K.L., Rosenberger, K.J., Paull, C.K., Gwiazda, R., Gales, J., Lorenson, T., Barry, J.P., Talling, P.J., McGann, M., Xu, J., Lundsten, E., Anderson, K., Litvin, S.Y., Parsons, D.R., Clare, M.A., Simmons, S.M., Sumner, E.J., Cartigny, M.J.B., 2019. Sediment and organic carbon transport and deposition driven

by internal tides along Monterey Canyon, offshore California. Deep Sea Research Part I: Oceanographic Research Papers 153, 103108.


Submarine canyons are globally important conduits for sediment and organic carbon transport into the deep sea. Using a novel dataset from Monterey Canyon, offshore central California, that includes an extensive array of water column sampling devices, we address how fine-grained sediment and organic carbon are transported, mixed, fractionated, and buried along a submarine canyon. Anderson-type sediment traps were deployed 10–300 m above the seafloor on a suite of moorings anchored between 278 and 1849 m water depths along the axial channel of Monterey Canyon during three consecutive 6-month deployments (2015–2017). Tidal currents within the canyon suspended and transported fine-grained sediment and organic carbon that were captured in sediment traps, which record the composition of sediment and organic carbon transport along the canyon. High sediment accumulation rates in traps increased up-canyon and near the seafloor, where fine-scale (<1 cm) layering was increasingly distinctive in CT scans. There was no along-canyon trend in the organic carbon composition (percent modern carbon and isotopic signatures) among trap locations, suggesting effective mixing. Organic carbon content (weight percent total organic carbon) and excess 210Pb activities (dpm/g) increased down-canyon, reflecting reduced flux of sediment and organic carbon into deeper water, more distal traps. Differing organic carbon signatures in traps compared with previous measurements of seabed deposits along Monterey Canyon suggest that organic carbon transported through the canyon with internal tides may not be consistently recorded in seafloor deposits. First-order estimates from comparing organic carbon content of core and trap samples results in low organic carbon specific burial efficiency (ranging from ~26% to ~0.1%) and suggests that the modern upper Monterey Canyon may not be an effective sink for carbon. Organic carbon isotopic signatures from sediment traps in the water column show more marine influence than seafloor sediment cores; this is likely due to the deposition and reworking of seafloor deposits by sediment density flows and preferential consumption of fresh marine organic carbon on the seafloor, which is better preserved in the traps. Sediment and remaining organic carbon in canyon floor and lower flank deposits preferentially reflect episodic sediment density flow events that are unrelated to internal tides. This study provides a quantified example and conceptual model for internal-tide-related sediment and organic carbon transport, mixing, and burial trends along a submarine canyon that are likely to be similar in many canyons worldwide.

Mariscal, C., Barahona, A., Aubert-Kato, N., Aydinoglu, A.U., Bartlett, S., Cárdenas, M.L., Chandru, K., Cleland, C., Cocanougher, B.T., Comfort, N., Cornish-Bowden, A., Deacon, T., Froese, T., Giovannelli, D., Hernlund, J., Hut, P., Kimura, J., Maurel, M.-C., Merino, N., Moreno, A., Nakagawa, M., Peretó, J., Virgo, N., Witkowski, O., Cleaves, H.J., 2019. Hidden concepts in the history and philosophy of origins-of-life studies: A workshop report. Origins of Life and Evolution of Biospheres 49, 111-145.

https://doi.org/10.1007/s11084-019-09580-x

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence

of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.



Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.

Marty, B., Bekaert, D.V., Broadley, M.W., Jaupart, C., 2019. Geochemical evidence for high volatile fluxes from the mantle at the end of the Archaean. Nature 575, 485-488.

https://doi.org/10.1038/s41586-019-1745-7

The exchange of volatile species—water, carbon dioxide, nitrogen and halogens—between the mantle and the surface of the Earth has been a key driver of environmental changes throughout Earth’s history. Degassing of the mantle requires partial melting and is therefore linked to mantle convection, whose regime and vigour in the Earth’s distant past remain poorly constrained. Here we present direct geochemical constraints on the flux of volatiles from the mantle. Atmospheric xenon has a monoisotopic excess of 129Xe, produced by the decay of extinct 129I. This excess was mainly acquired during Earth’s formation and early evolution, but mantle degassing has also contributed 129Xe to the atmosphere through geological time. Atmospheric xenon trapped in samples from the Archaean eon shows a slight depletion of 129Xe relative to the modern composition, which tends to disappear in more recent samples. To reconcile this deficit in the Archaean atmosphere by mantle degassing would require the degassing rate of Earth at the end of the Archaean to be at least one order of magnitude higher than today. We demonstrate that such an intense activity could not have occurred within a plate tectonics regime. The most likely scenario is a relatively short (about 300 million years) burst of mantle activity at the end of the Archaean (around 2.5 billion years ago). This lends credence to models advocating a magmatic origin for drastic environmental changes during the Neoarchaean era, such as the Great Oxidation Event.

Mastalerz, M., Drobniak, A., Ames, P., McLaughlin, P.I., 2019. Application of pXRF elemental analysis and organic petrography in correlation of Pennsylvanian strata: An example from the Indiana part of the Illinois Basin, USA. International Journal of Coal Geology 216, 103342.


The principal purpose of this research is to investigate whether elemental chemistry obtained by a portable X-ray fluorescence (pXRF) analyzer can aid in correlating lithostratigraphic units within the Pennsylvanian coal-bearing sequence of the eastern part of the Illinois Basin in Indiana. The study is based on data collected from four boreholes: Indiana Geological and Water Survey wells SDH-377 in Daviess County, SDH-379 in Pike County, SDH-383 in Posey County, and SDH-43 in Warrick County. The organic-matter-rich marine black shales and limestones are our special targets because they may represent valuable marker beds. Highly elevated U and Mo concentrations can be utilized to clearly identify the stratigraphic positions of the organic-matter-rich marine black shales in the succession from the oldest to the youngest: Sh1, Sh2, Sh3, and Sh4. Increased concentrations of both U and Mo provide further evidence for the deposition of these shales in anoxic environments. Variations in Ca and Mg concentrations aid in identifying limestone and dolomitic limestone horizons through the interval. Although the positions of marine shales and limestone strata were clearly defined based on pXRF data, identifying specific shales or limestones was problematic because of the wide elemental variations that exist within individual horizons. To help overcome this difficulty, reflected light microscopy was used as complementary technique on shale samples. These shales represent early oil window maturity(vitrinite reflectance 0.56 to 0.58%) and their organic matter is dominated by low-reflectance amorphous organic matter (AOM) and high-reflectance micrinized AOM. Well-preserved alginite, vitrinite, inertinite, and solid bitumen are rare. Our results show that proportions of low-reflectance AOM and micrinized AOM and framboidal pyrite content are promising characteristics that may help to identify individual shales. Specifically, Sh1 and Sh4 are

dominated by low-reflectance AOM, whereas the other two shales have micrinized AOM as the dominant component. Sh2 and Sh4 have consistently high framboidal pyrite content.



Dissolved organic matter (DOM) in groundwater is fundamentally important with respect to biogeochemical reactions, global carbon cycling, heavy metal transport, water treatability and potability. One source of DOM to groundwater is from the transport of organic matter from the vadose zone by rainfall recharge. Changes in precipitation patterns associated with natural climate variability and climate change are expected to alter the load and character of organic matter released from these areas, which ultimately impacts on groundwater quality and DOM treatability. In order to investigate potential changes in groundwater DOM character after rainfall recharge, we sampled shallow groundwater from a coastal peat-rich sand aquifer in New South Wales, Australia, during an extended period of low precipitation (average daily precipitation rate < 1.6 mm day−1 over the 8 months prior to sampling), and after two heavy precipitation events (84 mm day−1 and 98 mm day−1 respectively). We assess changes in DOM composition after correcting for dilution by a novel combination of two advanced analytical techniques: liquid chromatography organic carbon detection (LC-OCD) and negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We also assess changes in water chemistry pre- and post-rainfall. Post-rainfall, we show that the dilution-corrected amount of highly aromatic DOM molecular formulae (i.e. those categorised into the groups polyphenolics and condensed aromatics) were 1.7 and 2.0 times higher respectively than in pre-rainfall samples. We attribute this to the flushing of peat-derived DOM from buried organic material into the groundwater. We also identify that periods of low precipitation can lead to low hydrophilic/HOC ratios in groundwater (median = 4.9, n = 14). Redundancy analysis (RDA) was used to compare the HOC fraction with FT-ICR MS compound groups. We show that HOC has a more aromatic character in pre-rainfall samples, and is less similar to the aromatic groups in post-rainfall samples. This suggests that the decline in water-borne hydrophobics observed post-rainfall could be associated with preferential adsorption of the hydrophobic aromatic DOM, making post-rainfall samples less treatable for potable water supply. Post-rainfall we also observe significant increases in arsenic (leading to concentrations greater than 3 times the World Health Organisation drinking water limit of 10 μg/L). Increases in coastal rainfall due to climate change may therefore alter the composition of groundwater DOM in coastal peatland areas in ways that may impact DOM bioavailability, and increase arsenic concentrations, reducing the ease of water treatment for human consumption. To the best of our knowledge, this is the first study to identify the chemical and molecular changes of shallow groundwater DOM pre-rainfall and post-rainfall in a sedimentary organic carbon rich environment through multiple analytical techniques.

McMahon, S., 2019. Earth's earliest and deepest purported fossils may be iron-mineralized chemical gardens. Proceedings of the Royal Society B: Biological Sciences 286, 20192410.


Recognizing fossil microorganisms is essential to the study of life's origin and evolution and to the ongoing search for life on Mars. Purported fossil microbes in ancient rocks include common assemblages of iron-mineral filaments and tubes. Recently, such assemblages have been interpreted to represent Earth's oldest body fossils, Earth's oldest fossil fungi, and Earth's best analogues for fossils that might form in the basaltic Martian subsurface. Many of these putative fossils exhibit hollow circular cross-sections, lifelike (non-crystallographic, constant-thickness, and bifurcate) branching, anastomosis, nestedness within ‘sheaths’, and other features interpreted as strong evidence for a biological origin, since no abiotic process consistent with the composition of the filaments has been shown to produce these specific lifelike features either in nature or in the laboratory. Here, I show experimentally that abiotic chemical gardening can mimic such purported fossils in both morphology and composition. In particular, chemical gardens meet morphological criteria previously proposed to establish biogenicity, while also producing the precursors to the iron minerals most commonly constitutive of filaments in the rock record. Chemical gardening is likely to occur in nature. Such microstructures should therefore not be assumed to represent fossil microbes without independent corroborating evidence.

Medin, T., Martínez-Navarro, B., Madurell-Malapeira, J., Figueirido, B., Kopaliani, G., Rivals, F., Kiladze, G., Palmqvist, P., Lordkipanidze, D., 2019. The bears from Dmanisi and the first dispersal of early Homo out of Africa. Scientific Reports 9, 17752.

https://doi.org/10.1038/s41598-019-54138-6

We report on the taxonomy and paleodiet of the bear population that inhabited the emblematic palaeoanthropological Early Pleistocene (1.8 Ma) site of Dmanisi (Georgia), based on a dual approach combining morphometrics and microwear of upper and lower teeth. Given that the teeth of Ursus etruscus Cuvier, 1823 from Dmanisi show considerable size variability, their systematic position has been debated. However, a comparative study of the coefficients of variation for tooth size measurements in several modern bear species shows that the variability in tooth size of the ursid population from Dmanisi could result from sexual dimorphism. The analysis of tooth microwear indicates that these bears inhabited a mixed environment of open plain with forest patches, where they had a browsing diet with a substantial contribution of meat and/or fish. Comparative tooth morphometric analyses of modern ursids and fossil U. etruscus indicate that this extinct species had an omnivorous behavior similar to that of extant brown bears. The ecological interactions of the Dmanisi bears with other members of the large mammals community, including the first hominins that dispersed out of Africa, are discussed in the light of this new evidence.



The Paleocene high volatile B bituminous Raša coal, mined on the Istrian Peninsula, Croatia, for nearly 400 years up to 1999, is notable in having a superhigh organic sulfur (SHOS) content, exceeding 11% in some cases. The latter feature contributed to interest in the coal, far outweighing its status as a locally-used coal. Investigation by organic petrology, X-ray diffraction mineralogy, X-ray fluorescence and ICP-MS chemistry, SEM-EDS and TEM-EDS-SAED, micro-FTIR spectroscopy, and

Raman spectroscopy showed that the Raša coal is dominated by vitrinite-group macerals, CaO and SO3, carbonate minerals with contributions by Sr- and Ba-sulfates at the sub-micron scale, and the contribution of sulfur to the organic structure. Compared to Chinese SHOS coals and world ash, a majority of analyzed trace elements in Raša coal and ash, respectively, were depleted (up to 0.8 times), with the exception of V, Se, Sr, and Ba, which were increased 1.7 to 26 times. This fact, supported by elevated trace element concentrations in dripstone, are evidence for weathering of Raša coal by underground water, which is contaminating the local environment with trace elements, selenium in particular. Results of this study warrant further research.

Meng, X., Xie, R., Jia, H., Li, H., 2019. Identification of light oil in 2D NMR spectra of tight sandstone reservoirs by using L1/L2 two-parameter regularization. Energy & Fuels 33, 10537-10546.


This work presents L1/L2 two-parameter regularization as an efficient technique for the identification of light oil in the two-dimensional (2D) nuclear magnetic resonance (NMR) spectra of tight sandstone reservoirs. A 2D NMR T2-T1 distribution model containing light oil, natural gas, and formation water is constructed. 2D NMR echo trains are obtained by means of the multiwaiting time Carr, Purcell, Meiboom, and Gill pulse sequence. A detailed analysis of the ill-posed characteristics to obtain 2D NMR spectrum is given using a Picard curve. The identification abilities of L1/L2 two-parameter regularization and three other techniques are compared in detail. The paper demonstrates that even if the signal-to-noise ratio (SNR) is around 100, it is still very difficult to obtain the 2D NMR spectrum. Light oil cannot be distinguished using Tikhonov regularization and truncated singular value decomposition. Both L1/L2 two-parameter regularization and L1 norm regularization can identify light oil, while the identification ability of L1/L2 two-parameter regularization is higher than that of L1 norm regularization, especially when the SNR is very low. L1/L2 two-parameter regularization can be used as an effective technique to identify light oil from formation water in the 2D NMR spectra of tight sandstone reservoirs.

Miggiels, P., Wouters, B., van Westen, G.J.P., Dubbelman, A.-C., Hankemeier, T., 2019. Novel technologies for metabolomics: More for less. TrAC Trends in Analytical Chemistry 120, 115323.


The human metabolome provides a direct physiological read-out of an individual's actual health state and includes biomarkers that may predict disease or response to a treatment. The discovery and validation of these metabolomic biomarkers requires large-scale cohort studies, typically involving thousands of samples. This analytical challenge drives novel technological developments to enable faster, cheaper, and more comprehensive metabolomic analysis: more for less.

This review summarises recent (2012–2018) developments towards this goal in all aspects of the analytical workflow, in relation to NMR but primarily to mass spectrometry (MS). Recent trends include miniaturisation and automation of extraction techniques, online coupling to fast analysis methods including direct infusion ion mobility MS, integrated microfluidic devices, and sharing and standardizing metabolomics software and data.

The technological advances in metabolomics support its widespread application, integration with other -omics fields, and ultimately disease prediction and precision medicine.

Millán-Aguiñaga, N., Soldatou, S., Brozio, S., Munnoch, J.T., Howe, J., Hoskisson, P.A., Duncan, K.R., 2019. Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential. Microbiology 165, 1169-1180.

https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000845

Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales , within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare A ctinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia . This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.

Mishin, A.S., Dubinich, V.N., Svarovskaya, N.A., Dadashev, M.N., Khlebnikov, V.N., 2019. Features of the methods for the production of viscous oil from oil rims of the Cenomanian horizon. Chemistry and Technology of Fuels and Oils 55, 424-431.

https://doi.org/10.1007/s10553-019-01047-z

The methods of extracting viscous oil from oil leg reservoir (oil rims) of the Cenomanian horizon are experimentally investigated (PK layers). It was found that steam contributes to the swelling and dispersion of clay components of the rock, i.e. thermal methods cannot be recommended for use. The effect of oil on the rock properties of PK layers was investigated. It was shown that permeability, wettability and degree of oil displacement by saline water depend on oil saturation, and the rock transition from hydrophilicity to hydrophobicity occurs at oil saturation above 75%. Alkaline flooding and the use of non-ionic surfactants are not effective for enhancing the recovery of PK layers. For oil displacement, it is recommended to apply a water-gas mixture or sequentially inject solvent and water (or water-gas mixture). Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 4, pp. 42 – 46, July – August, 2019.


https://doi.org/10.1038/s41598-019-51796-4

In response to recent advances in understanding relating to the remarkable persistence of soil organic matter during burial and diagenesis, we examine the extent to which bitumen compositionally reflects the soil organic matter from which it was derived. Through a simple set of experiments, exposure of bitumen to lipase and cellulase, two enzymes effective in the biodegradation of soil organic matter, resulted in the release of glycerin, palmitic and oleic fatty acids from lipase digestion in addition to the release of glucose, alkylphenols and acyclic polyols from fermentation with cellulase, consistent with the products expected these enzymes. These results are significant in that they suggest that heavy oils are more similar to their soil precursor than previously thought, that biodegradation of bitumen can be accelerated using common over the counter enzymes in aerobic conditions and that heavy oils, which are 1000 times more abundant than coal, can release similar biomolecules as those generated in bioreactor culture or biomass harvest, using two of the most abundantly produced enzymes presently available.

Misra, S., Das, S.K., Varma, A.K., Mani, D., Kalpana, M.S., Ekblad, A., Biswas, S., 2020. Multi-proxy approach on the hydrocarbon generation perspective of Barjora Basin, India. Marine and Petroleum Geology 112, 104108.


Barjora Basin in India is a small basin characterized by a high organic richness of early mature nature. The present study aims to find the source of organic matter (OM) and hydrocarbon generation potential of Barjora Basin. Systematically collected coal and shale samples from R-II seam of the basin were used for proximate and ultimate analyses, Rock Eval pyrolysis along with total organic carbon (TOC) content, organo-micropetrographic framework, thermal maturity, carbon isotopic signature, biomarker composition, functional group studies and estimation of relative aliphaticity and aromaticity through Fourier Transform infrared spectroscopy (FTIR). The novelty of the present work lies in the application of multiple proxies such as stable isotope ratio of organic carbon (δ13C), biomarker signatures, thermal maturity parameters, organo-micropetrography and estimation and quantification of functional groups for palaeoenvironmental reconstruction and to assess the hydrocarbon productivity of the basin. A dominant terrestrial OM input in Barjora Basin is indicated by the TOC to total nitrogen ratio (C/N), δ13C and biomarker compositions. High gelification index (GI), tissue preservation index (TPI), and carbon preference index (CPI) values indicate that coals are deposited in wet swamp forest regime under high rainwater conditions and shales are formed in upper delta plain regime under high groundwater activity. In addition, large liptinite content, TPI and GI designate short transportation of the OM before burial leading to organic richness of the Barjora Basin. Moreover, high liptinite content, type II-III admixed kerogen input, S2/S3 ratio, TPI and index for hydrocarbon generation (IHG) signify higher potential of the basin for hydrocarbon generation.

Mittnik, A., Massy, K., Knipper, C., Wittenborn, F., Friedrich, R., Pfrengle, S., Burri, M., Carlichi-Witjes, N., Deeg, H., Furtwängler, A., Harbeck, M., von Heyking, K., Kociumaka, C., Kucukkalipci, I., Lindauer, S., Metz, S., Staskiewicz, A., Thiel, A., Wahl, J., Haak, W., Pernicka, E., Schiffels, S., Stockhammer, P.W., Krause, J., 2019. Kinship-based social inequality in Bronze Age Europe. Science 366, 731-734.


Abstract: Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.

Editor's Summary: Ancient DNA informs on past cultures. Archaeology has used analysis of the artifacts and remains of people to uncover their past behaviors and to infer their cultural practices. However, establishing genetic relationships has only recently become possible. Mittnik et al. examined the kinship and inheritance of the remains of people from the German Lech River Valley over a time period spanning the Late Neolithic Corded Ware Culture, the Bell Beaker Complex, the Early Bronze Age, and the Middle Bronze Age (see the Perspective by Feinman and Neitzel). From genetic and archaeological analyses, it was revealed that the Early Bronze Age household's burials over multiple generations consisted of a high-status core family and unrelated low-status individuals. Furthermore, women were not related to the men within the household, suggesting that men stayed within their birth communities in this society, but women did not.

Mohajeri, M., Shariatipour, S., 2019. Evaluation of enhancing CO2 sequestration by post-brine injection under different scenarios using the E300 compositional simulator. Petroleum Research 4, 314-333.


To accelerate the CO2 trapping in geological storage sites, several injection strategies have been proposed by researchers so far. However, the question remains unanswered as to which one of these injection strategies is the most efficient in terms of immobilising CO2 and more importantly, how these strategies might be improved. In this paper, we attempt to simulate a typical geological CO2 storage scheme in an aquifer using the E300 compositional reservoir simulator and subsequently investigate and compare the impact of various injection strategies on CO2 immobilising efficiency. Secondly, the impact of adding a short period of post-brine injection on various strategies is newly investigated.

Our results reveal that using a relatively short period of post-brine injection can significantly improve total CO2 trapping efficiency in all the strategies. In general, by using post injection of brine, more CO2 is spread out through the aquifer and, as a consequence, by increasing the interfacial area of the CO2 plume, the amount of dissolution as a result of mass transfer increases significantly. Moreover, the effect of convection can become stronger in the case of post-brine injection creating a stronger density instability and thus a more rapid initiation of convection. Furthermore, when brine is injected into the system, CO2 is displaced away from the well resulting in a forced imbibition process and thereby enhancing the capillary trapping efficiency. The post-injection of brine has also one more particular effect in strategies of horizontal injection and simultaneous CO2/brine injection in different intervals. In this regard, post-brine injection creates a stronger downward pressure gradient that counters the tendency of the CO2 plume to rise and therefore retards the CO2 in

reaching the top of the aquifer. This increases the time that the CO2 can be in contact with the fresh formation brine and so enhances the trapping efficiency.

We envisage that the post-brine injection could enhance the total trapping efficiency of CO2 from 26%, 30.8%, 39.8% and 59.1% to 47.7%, 44.2%, 62% and 63.9%, when it was added into different strategies of CO2 continuous injection, simultaneous injection of CO2/brine in the same and different intervals and a horizontal system, respectively. However, our findings show that the effectiveness of post-brine injection may be reduced in high vertical permeability values and in this respect, capillary trapping can be more affected by vertical permeability variation. Furthermore, the results show that selection of the rate and duration of post-brine injection can have considerable effects on total CO2 trapping efficiency.

Mohanty, K.K., Tong, S., Miller, C., Zeng, T., Honarpour, M.M., Turek, E., Peck, D.D., 2019. Improved hydrocarbon recovery using mixtures of energizing chemicals in unconventional reservoirs. SPE Reservoir Evaluation & Engineering 22, 1436-1448.

https://doi.org/10.2118/187240-PA

The objective of this work is to design and evaluate an effective blend of chemicals that can be injected into shale (black oil or critical fluid) reservoirs to enhance hydrocarbon recovery. The blend can be implemented as a prepad fluid ahead of hydraulic-fracturing fluid or as a remedial fluid later in the life of a well. A chemical blend (CB) consisting of an organic solvent (OS), a surfactant, and an oxidizing agent (OA) (in conjunction with an acid) was designed, developed, and tested in the laboratory on crushed rocks, core plugs, and fractured cores to evaluate the interactions of the chemicals with the shale samples. Microcomputed-tomography (micro-CT) scanning, scanning electron microscopy, and Brinell hardness tests were used to evaluate surface changes in the shales.

The results of laboratory experiments demonstrate that the CB extracts up to 30% of mobile oil in crushed rocks and improves permeability by 25 to 100% in thin core plugs. Some of the mechanisms that might support the CB application are as follows: (1) pressurization of the formation and reopening of the closed fractures, thus improving well productivity; (2) extraction and mobilization of low-mobility oil, remnants of the original kerogen, removal of deposited salt, and trapped water in matrix and fracture network that impedes fluid flow; (3) creation of pathways to high-pressure liquid-rich small organic pores, where hydrocarbon liquids are trapped, adsorbed, and dissolved in the kerogen; (4) creation of flow pathways for the intrusion of aqueous-based fluids in oil-wet organic-rich rocks with wettability alteration to accelerate the injection, countercurrent imbibition, and osmotic processes; and (5) enhancement of porosity and permeability of fracture surfaces by the introduction of a delayed reaction mechanism to deliver acids deeper into the microfracture network without compromising rock mechanical properties. The presence of sulfate ions in the OA did not contribute to any noticeable scale deposit while delaying the reactivity of acid with inorganic components of shale surfaces. Several field trials have been conducted successfully in the Eagle Ford (EF) Formation.

Moridis, G.J., Reagan, M.T., Queiruga, A.F., Boswell, R., 2019. Evaluation of the performance of the oceanic hydrate accumulation at site NGHP-02-09 in the Krishna-Godavari Basin during a production test and during single and multi-well production scenarios. Marine and Petroleum Geology 108, 660-696.


The objective of this study is to quantify, by means of numerical simulation, the response of the complex system of gas hydrate accumulations at Site NGHP-02-09, Krishna-Godavari Basin, Indian Ocean, to different production conditions, and to determine the technical feasibility of gas production through depressurization-induced dissociation. The study assesses the suitability of the site for a long-term production test involving a single vertical well, and the long-term potential of the deposit under full-field production using a system of multiple vertical wells. We simulate gas and water flow, estimate the production performance of the accumulation and separately investigate the corresponding geomechanical response of the system. Results indicate that production from Site NGHP-02-09 under the conditions of a long-term field test involving a single vertical well is technically feasible and can yield high gas production rates. However, an inability to fully isolate the water bearing zones results in production that is largely from dissolved gas rather than hydrate dissociation and is thus burdened by excessive water production. Given the estimated physical properties of the reservoir system, Site NGHP-02-09 does not appear to be a promising location for a single-well field test of gas production, but may be a promising production target for full-field production operations using a multi-well system in which exterior wells can mitigate water inflows to allow interior wells to more effectively depressurize the formation and capture methane from gas hydrate dissociation. Geomechanical issues need to be carefully considered as significant displacements are possible, which can be challenging to well construction and stability.

Moroeng, O.M., Mhuka, V., Nindi, M.M., Roberts, R.J., Wagner, N.J., 2019. Comparative study of a vitrinite-rich and an inertinite-rich Witbank coal (South Africa) using pyrolysis-gas chromatography. International Journal of Coal Science & Technology 6, 621-632.

https://doi.org/10.1007/s40789-019-00274-3

This study aims to compare iso-rank vitrinite-rich and inertinite-rich coal samples to understand the impact of coal-forming processes on pyrolysis chemistry. A medium rank C bituminous coal was density-fractionated to create a vitrinite-rich and an inertinite-rich sub-sample. The vitrinite-rich sample has 83 vol% total vitrinite (mineral-matter-free basis), whereas the inertinite-rich counterpart has 66 vol% total inertinite. The vitrinite-rich sample is dominated by collotelinite and collodetrinite. Fusinite, semifusinite, and inertodetrinite are the main macerals of the inertinite-rich sample. Molecular chemistry was assessed using a pyrolysis gas chromatograph (py-GC) equipped with a thermal desorption unit coupled to a time of flight mass spectrometer (MS) (py-GC/MS) and solid-state nuclear magnetic resonance (13C CP-MAS SS NMR). The pyrolysis products of the coal samples are generally similar, comprised of low and high molecular weight alkanes, alkylbenzenes, alkylphenols, and alkyl-subtituted polycyclic aromatic hydrocarbons, although the vitrinite-rich sample is chemically more diverse. The lack of diversity exhibited by the inertinite-rich sample upon pyrolysis may be interpreted to suggest that major components were heated in their geologic history. Based on the 13C CP-MAS SS NMR analysis, the inertinite-rich sample has a greater fraction of phenolics, reflected in the py-GC/MS results as substituted and unsubstituted derivatives. The greater abundance of phenolics for the inertinite-rich sample may suggest a fire-related origin for the dominant macerals of this sample. The C2-alkylbenzene isomers (p-xylene and o-xylene) were detected in the pyrolysis products for the vitrinite-rich and inertinite-rich samples, though more abundant in the former. The presence of these in both samples likely reflects common source vegetation for the dominant vitrinite and inertinite macerals.

Motie, M., Assareh, M., 2020. CO2 sequestration using carbonated water injection in depleted naturally fractured reservoirs: A simulation study. International Journal of Greenhouse Gas Control 93, 102893.


In this work, the focus is given to the study of sequestration potential and recovery improvement in depleted NFRs using CWI. Initially a number of CWI experiments on reservoir cores with different wettabilities were modeled to verify physical aspect of the suggested simulation approach. Afterward, a modeling procedure was suggested to make an insight into the engineering parts of this process. In summary, it defined a 3 × 3×3[m3] reservoir rock matrix (a single matrix block, SMB) surrounded by carbonated water in fractures. The numerical aspects of the model were verified by a mesh independent study, in addition. The effects of several key parameters such as anisotropy, permeability, CO2 fraction in water, wettability alteration and block height were studied and compared for matrix blocks with different wettabilities. These effects were studied by incremental oil recovery and the amount of trapped CO2 in the matrix block. As indicated in this study, by implementing CWI, 10.6% incremental oil recovery can be achieved for a water-wet sample and 4.7% for an oil-wet sample during a period of 10 years. Moreover, about 3000[mol] CO2 were trapped in oil and water of the matrix after 10 years and this was increased to more than 8000[mol] after 100 years for the water-wet matrix block with a volume of 27[m3]. During the same period, by increasing the CO2 concentration from 1% to 2% in CW, oil recovery factor increased by 8.4% in water-wet sample. Subsequently, the amount of trapped CO2 grew from 850 to 3000[mol] in 10 years.


http://science.sciencemag.org/content/366/6469/eaay3134.abstract

Abstract: The dense circuit structure of mammalian cerebral cortex is still unknown. With developments in three-dimensional electron microscopy, the imaging of sizable volumes of neuropil has become possible, but dense reconstruction of connectomes is the limiting step. We reconstructed a volume of ~500,000 cubic micrometers from layer 4 of mouse barrel cortex, ~300 times larger than previous dense reconstructions from the mammalian cerebral cortex. The connectomic data allowed the extraction of inhibitory and excitatory neuron subtypes that were not predictable from geometric information. We quantified connectomic imprints consistent with Hebbian synaptic weight adaptation, which yielded upper bounds for the fraction of the circuit consistent with saturated long-term potentiation. These data establish an approach for the locally dense connectomic phenotyping of neuronal circuitry in the mammalian cortex.

Structured Abstract

Introduction: The brain of mammals consists of an enormously dense network of neuronal wires: the axons and dendrites of nerve cells. Their packing density is so high that light-based imaging methods have so far only been able to resolve a very small fraction of nerve cells and their interaction sites, the synapses, in mammalian cortex. Recent advances in three-dimensional (3D) electron microscopy allow researchers to image every nerve cell and all chemical synapses in a given

piece of brain tissue, opening up the possibility of mapping neuronal networks densely, not just sparsely. Although there have been substantial advances in imaging speed, the analysis of such 3D image data is still the limiting step. Therefore, dense reconstructions of cortical tissue have thus far been limited to femtoliter-scale volumes, keeping the systematic analysis of axons, neuronal cell bodies and their dendrites of different types, and the dense connectome between them out of reach.

Rationale: Image analysis has made decisive progress using artificial intelligence–based methods, but the resulting reconstructions of dense nerve tissue are still too error-prone to be scientifically meaningful as is. To address this, human data analysis has been integrated into the generation of connectomes and it is the efficiency of this human–machine data analysis that now determines progress in connectomics. We therefore focused on efficiency gains by: (i) improving the automated segmentation quality, (ii) analyzing the automated segmentation for locations of likely errors and directing the human work to these locations only, and (iii) optimizing human data interaction by helping annotators to immediately understand the problem to be solved, allowing fast, in-browser parallel data flight, and by minimizing latency between annotator queries. With this, close to 100 student annotators solved hundreds of thousands of reconstruction problems within just 29 s each, including all preparation and transition time.

Results: We reconstructed 2.7 m of neuronal wires densely in layer 4 of mouse somatosensory cortex within only ~4000 invested human work hours, yielding a reconstruction ~300 times larger than previous dense cortical reconstructions at ~20-fold increased efficiency, a leap for the dense reconstruction of connectomes. The resulting connectome between 6979 presynaptic and 3719 postsynaptic neurites with at least 10 synapses each, comprising 153,171 synapses total, was then analyzed for the dense circuit structure in the cerebral cortex. We found that connectomic data alone allowed the definition of inhibitory axon types that showed established principles of synaptic specificity for subcellular postsynaptic compartments, but that at scales beyond ~5 μm, geometric predictability of the circuit structure was low and coarser models of random wiring needed to be rejected for dense cortical neuropil. A gradient of thalamocortical synapse density along the cortical axis yielded an enhanced variability of synaptic input composition at the level of single L4 cell dendrites. Finally, we quantified connectomic imprints consistent with Hebbian synaptic weight adaptation, obtaining upper bounds for the fraction of the circuit that could have undergone long-term potentiation.

Conclusion: By leveraging human–machine interaction for connectomic analysis of neuronal tissue, we acquired the largest connectome from the cerebral cortex to date. Using these data for connectomic cell-type definition and the mapping of upper bounds for the learned circuit fraction, we establish an approach for connectomic phenotyping of local dense neuronal circuitry in the mammalian cortex, opening the possibility for the connectomic screening of nervous tissue from various cortices, layers, species, developmental stages, sensory experience, and disease conditions.

Editor's Summary. Brain anatomy revealed in startling detail. The mammalian cerebral cortex is an enormously complex network of neuronal processes that are long and thin, branching, and extremely densely packed. This high packing density has made the reconstruction of cortical neuronal networks challenging. Motta et al. used advanced automated imaging and analysis tools to reconstruct with high spatial resolution the morphological features of 89 neurons and their connections in the mouse barrel cortex. The reconstruction covered an area more than two orders of magnitude larger than earlier neuroanatomical mapping attempts. This approach revealed

information about the connectivity of inhibitory and excitatory synapses of corticocortical as well as excitatory thalamocortical connections.


https://doi.org/10.1007/s00203-019-01705-0

Tanneries are the primary source of toluene pollution in the environment and toluene due to its hazardous effects has been categorized as persistent organic pollutant. Present study was initiated to trace out metabolic fingerprints of three toluene-degrading bacteria isolated from tannery effluents of Southern Punjab. Using selective enrichment and serial dilution methods followed by biochemical, molecular and antibiotic resistance analysis, isolated bacteria were subjected to metabolomics analysis. GC–MS/LC–MS analysis of bacterial metabolites helped to identify toluene transformation products and underlying pathways. Three toluene-metabolizing bacteria identified as Bacillus paralicheniformis strain KJ-16 (IUBT4 and IUBT24) and Brevibacillus agri strain NBRC 15538 (IUBT19) were found tolerant to toluene and capable of degrading toluene. Toluene-degrading potential of these isolates was detected to be IUBT4 (10.35 ± 0.084 mg/h), IUBT19 (14.07 ± 3.14 mg/h) and IUBT24 (11.1 ± 0.282 mg/h). Results of GC–MS analysis revealed that biotransformation of toluene is accomplished not only through known metabolic routes such as toluene 3-monooxygenase (T3MO), toluene 2-monooxygenase (T2MO), toluene 4-monooxygenase (T4MO), toluene methyl monooxygenase (TOL), toluene dioxygenase (Tod), meta- and ortho-ring fission pathways. But additionally, confirmed existence of a unique metabolic pathway that involved conversion of toluene into intermediates such as cyclohexene, cyclohexane, cyclohexanone and cyclohexanol. LC–MS analysis indicated the presence of fatty acid amides, stigmine, emmotin A and 2, 2-dinitropropanol in supernatants of bacterial cultures. As the isolated bacteria transformed toluene into relatively less toxic molecules and thus can be preferably exploited for the eco-friendly remediation of toluene.

Mukhopadhyay, D.K., 2019. Petroleum system in Indian Collision Zone: Perspective from structural geology. Journal of the Geological Society of India 94, 549-549.

https://doi.org/10.1007/s12594-019-1356-9

No abstract

Müller, S., Arfai, J., Jähne-Klingberg, F., Bense, F., Weniger, P., 2020. Source rocks of the German Central Graben. Marine and Petroleum Geology 113, 104120.


Jurassic to Lower Cretaceous formations are the most important source rocks for hydrocarbons in the southern Central Graben area. Within the Dutch Central Graben, the Lower Jurassic Posidonia Shale Formation is the most prolific source for hydrocarbons, while the Upper Jurassic to Lowermost Cretaceous Bo Member of the Farsund Formation plays this role in the Danish Central Graben. Oil and gas discoveries in the Norwegian, Dutch and Danish part of the Central Graben proved a prolific petroleum system. Despite limited success of hydrocarbon exploration in the German part of the

Central Graben, various indications suggest migration of gas out of active thermogenic source rocks that are closely related to potential shallow gas accumulations. These indications include the restricted location of the bright spots above the Jurassic graben system, the occurrence of gas chimneys underneath these accumulations and geochemical data from offshore The Netherlands, which support contribution of thermogenic gas. The purpose of this study is to assess the potential for generating thermogenic hydrocarbons from Upper Triassic to Lower Cretaceous formations. For this reason, prominent source rocks of the Southern North Sea, i.e. the Posidonia Shale Formation and the Upper Jurassic to Lower Cretaceous “Hot Shales” (namely Clay Deep Member offshore The Netherlands and Bo Member offshore Denmark), were mapped in detail. These and other potential formations from the Late Triassic to the Early Cretaceous are integrated into an existing petroleum system model of the Northern German North Sea, which was modified for the new requirements. The results showed that the main source rocks of the southern Central Graben, the Posidonia Shale Formation, and the Upper Jurassic – Lower Cretaceous “Hot Shales” are insignificant as sources for commercial hydrocarbon accumulations within the German Central Graben area. That is either due to marginal occurrence or to low maturity. However, Lower to Upper Jurassic formations such as marine claystones of the Aalburg Formation and the lower parts of the Kimmeridge Clay Formation, as well as coaly intervals of the Central Graben Subgroup, are likely to have generated, and still generate, hydrocarbons.

Müller, V., 2019. New horizons in acetogenic conversion of one-carbon substrates and biological hydrogen storage. Trends in Biotechnology 37, 1344-1354.


Strictly anaerobic, acetogenic (acetate-forming) bacteria are characterized by a reductive pathway in which two mol of CO2 are reduced to one mol of acetyl coenzyme A (acetyl-CoA) and then further to acetate, ethanol, or butyrate. Therefore, they have come into focus for an alternative, CO2-based bioeconomy. Other one-carbon (C1) substrates, such as formic acid or methanol, are promising feedstocks for an alternative bioeconomy using acetogens as biocatalysts that have been somewhat overlooked. In addition, acetogens, such as Acetobacterium woodii and Thermoanaerobacter kivui, have a unique enzyme system capable of reducing CO2 to formate with H2 as reductant that is superior over any chemical catalyst for CO2-based hydrogen storage. Therefore, acetogens are also promising candidates in the hydrogen economy as potential catalysts for hydrogen storage or production.

Muraoka, M., Ohtake, M., Susuki, N., Morita, H., Oshima, M., Yamamoto, Y., 2019. Thermal properties of highly saturated methane hydrate-bearing sediments recovered from the Krishna–Godavari Basin. Marine and Petroleum Geology 108, 321-331.


We measured the thermal constants (including conductivity, specific heat, and thermal diffusivity) of methane hydrate (MH)–bearing sediment samples recovered in 2015 from the Krishna–Godavari Basin, in India. These samples were recovered through the National Gas Hydrate Program Expedition 02 (NGHP-02). The measurements were performed using the single-sided Transient Plane Source (TPS) method. To investigate the influence of the sediment composition on the thermal properties of MH-bearing sediments, the thermal constants of MH-bearing sediments were measured at 5 °C

and 10 MPa over a porosity (ϕ) range of 41% ≤ ϕ ≤ 51% and MH saturation (Sh) range of 17% ≤ Sh ≤ 74%. In addition, density and mineral compositional measurements of the dry sediment grain samples were conducted.

The measured thermal conductivity slightly decreases with increasing ϕ and is independent of Sh. The measured specific heat increased with increasing ϕ, whereas it decreased with increasing Sh. The measured thermal diffusivity decreased with increasing ϕ, whereas it increased with increasing Sh. Various models were used to estimate the thermal constants to examine the applicability of these models to natural MH-bearing sediments. The distribution model (using a geometric mean model) is valid from the low to high MH saturations; however, the thermal properties of clay-rich layers are not likely reproducible by the distribution model from the mineral compositions. This indicates that the low value of the observed thermal conductivity in the clay-rich samples is likely a product of the sediment's small grain size.

Myshakin, E.M., Seol, Y., Lin, J.-S., Uchida, S., Collett, T.S., Boswell, R., 2019. Numerical simulations of depressurization-induced gas production from an interbedded turbidite gas hydrate-bearing sedimentary section in the offshore India: Site NGHP-02-16 (Area-B). Marine and Petroleum Geology 108, 619-638.


The recent National Gas Hydrate Program Expedition 02 (NGHP-02) identified the existence of gas hydrate-bearing sand reservoirs at a number of sites in the offshore of India including Site NGHP-02-16 in Area-B of the Krishna-Godavari Basin. The architecture of that gas hydrate accumulation is characterized by thin, gas hydrate-bearing, high quality sand layers interbedded with mud layers within a turbidite sedimentary interval. The lowest gas hydrate-bearing layer contacting a thinly-interbedded saline aquifer designates the base of the gas hydrate stability zone (BGHSZ). The proximity of the BGHSZ and the average temperature around 20 °C make the reservoir a favorable target for hydrate destabilization by means of the depressurization method. The results of the reservoir simulations indicate high gas production potential from this marine gas hydrate deposit with manageable concomitant water production using a well completion design that hydraulically isolates layers with water-saturated sands. Using a detailed geological input model, the predicted cumulative gas rates reach ∼3.1 × 104 m3/day (∼1.1 MMscf/day) after 90 days of continuous depressurization and demonstrate sustained production rates ∼3.0 × 104 m3/day (∼1.0 MMscf/day) after 5 years of production. The interbedded nature of this gas hydrate occurrence promotes the development of horizontal dissociation interfaces between gas hydrate-bearing sand and mud layers. As a result, non-uniform gas production along the horizontal interfaces becomes a primary determinant of reservoir performance. Simulation cases have been executed to determine the impact of the uncertainty in in situ reservoir permeability and the manner in which intrinsic permeability dynamically changes during dissociation in response to the imposed effective stress increase. The cases based on low initial effective permeability and high sensitivity of compaction to stress result in the least favorable production predictions.

Nakaya, Y., Nakashima, S., Otsuka, T., 2019. Evaluation of kinetic competition among formation and degradation processes of dissolved humic-like substances based on hydrothermal reactions measured by ultraviolet-visible spectroscopy. Geochemical Journal 53, 407-414.

http://www.terrapub.co.jp/journals/GJ/abstract/5306/53060407.html

Hydrothermal decolorization (color loss) of Nordic fulvic and humic acid solutions at 80-180°C for 0-600 hours was traced by ultraviolet-visible (UV-Vis) spectroscopy. These changes were considered to be due to degradation of humic-like chemical structure and represented by decreases in absorbance at 254 nm (UV254). The temperature dependence of their apparent rate constants obtained by the first order reaction model was well described by the Arrhenius equation giving activation energies of 87.6 and 101 kJ mol-1 for degradation of fulvic and humic acids, respectively. The degradation rates of humic substances were slower than the formation rates of humic-like substances by the Maillard-type browning reaction, suggesting that humic-like substances can be preserved in the aquatic environments, where their formation (browning) and degradation (decolorization) processes are occurring together. By extrapolation to 15°C of the Arrhenius equation, 99-1980 years of time scales for these processes were estimated. A time scale of changes in UV254 in natural aquatic environments estimated by kinetic analyses on Ago Bay bottom sediments (18 years) were closer to the formation time scales of humic-like substances.

Nanda, J., Shukla, K.M., Lall, M.V., Yadav, U.S., Kumar, P., 2019. Lithofacies characterization of gas hydrate prospects discovered during the National Gas Hydrate Program expedition 02, offshore Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 226-238.


Lithofacies of host sediments associated with gas hydrate reservoirs may have a significant influence on the formation of hydrates. The type of sediments and the depositional processes responsible for the gas hydrate-bearing sediments along the eastern margin of the India have been studied by integrating core data and logging-while-drilling downhole logs. Borehole data correlated with seismic data were used for the interpretation of geological process responsible for gas hydrate formation. The acquired seismic profiles were correlated with the downhole logs by identifying the shape of the well logs curves that indicate finning up and blocky patterns. Turbidite sands and debris flows were also identified from the log and core sediment studies. This study identified two prominent types of depositional systems: (1) turbidity currents and (2) debris flows were mainly responsible for the deposition of gas hydrate-bearing reservoirs in the study area. Based on these studies two well-developed gas hydrate systems have been identified in the Krishna-Godavari Basin and hydrates were determined to be distributed mostly in sand dominated facies. Fine-grained sand in the identified turbidite deposits were shown to be a good hydrate reservoir. The hydrate-bearing sediments in the central part of the Krishna-Godavari Basin (Area C in D6 block) consist of mostly debris flows, which is consistent with scattered gravel- and sand/silt-sized grains in channel-levee systems.

Nandimandalam, H., Gude, V.G., 2019. Indigenous biosensors for in situ hydrocarbon detection in aquatic environments. Marine Pollution Bulletin 149, 110643.

http://www.sciencedirect.com/science/article/pii/S0025326X1930791X

The use of microbial biofilms for the detection of hydrocarbon contamination in aquatic environments was investigated in this study. Two different microbial biofilms consisting of mixed culture bacteria and microalgae were used as biocatalysts and sensing organisms in the anode and

cathode chambers of a bioelectrochemical system, respectively. A series of experiments were conducted to evaluate the potential of this method for sensing hydrocarbon contamination and to study the effect of gasoline (varied between 0.04% (v/v) and 1% (v/v)) and background chemical oxygen demand (COD) concentrations on the sensor response. A linear relationship was observed for gasoline concentrations between 0 and 0.1% (v/v), while an exponential relationship was noted for the gasoline concentration in the range of 0 to 1% (v/v). Reproducibility and resilience of the biosensor in detecting the presence of hydrocarbons were studied. Finally, the ability of the biosensor to remove COD (∼70%) indicated its possible use in the bioelectrochemical treatment of polluted waters.

Nascimento-Dias, B.L.d., Andrade, M.B.B.d., da Costa Ludwig, Z.M., 2019. Analysing the astrobiological aspects through the comparison of pyroxenes detected in meteorites and Martian environments. International Journal of Astrobiology 18, 547-551.

https://doi.org/10.1017/S1473550419000041

Although pyroxenes are found abundantly in igneous rocks, this mineral group stands out for being one of the ferromagnesian mineral groups that constitute rocks of several different compositions. Hence, the purpose of this work is to demonstrate how these minerals may be relevant to Astrobiology. Essentially, through geochemical analyses of pyroxenes detected in Martian meteorites, it may be possible to find evidence of the existence of water in hydrothermal flows located in deep regions below the Martian surface. To this extent, it is also very important to highlight the whole collection of observational data from Mars, in which it is possible to notice that pyroxenes are found in a wide variety of geological environments. Therefore, based on Martian surface observations, meteorite analysis and experimental data, it is conceivable that, given the appropriate conditions, pyroxenes might be related to the formation and release of water molecules in the Martian environment.

Nash, W.J., Dunn, W.B., 2019. From mass to metabolite in human untargeted metabolomics: Recent advances in annotation of metabolites applying liquid chromatography-mass spectrometry data. TrAC Trends in Analytical Chemistry 120, 115324.


The relatively unbiased study of metabolites in biological systems is called untargeted metabolomics and the application of liquid chromatography-mass spectrometry platforms for data acquisition is now common across the world. When operating in its most unbiased form, this experimental strategy starts from assuming no knowledge of the metabolites to be detected and instead the data acquired is used to annotate or identify the detected metabolites on a study-by-study basis. The process of metabolite annotation is a bottleneck in untargeted metabolomics and to which significant progress has been made in the last ten years in understanding the limitations and developing new experimental and computational methods and tools to enhance our capabilities. In this review we will describe the current status of tools applied for metabolite annotation and discuss current areas where further work is required.

Nazir, A., Iqbal, M., Siddique, A., Ahmed, W., 2020. Evaluation of source, depositional environment, thermal maturity and biodegradation of organic matter from Kohat-Potwar Basin, Pakistan. Petroleum Science and Technology 38, 106-115.

https://doi.org/10.1080/10916466.2019.1684946

The study focusses on investigation of source rock generative characteristics and nature of crude oils from Upper Indus Basin (UIB), Pakistan. The source rock sediments and crude oil samples were geochemically analyzed. These samples belong to Lockhart, Patala, Datta and Kingriali formations from Kohat-Potwar region. The sediments samples were extracted using soxhlet extractor with organic solvents. Soluble organic matter (SOM) and crude oil were fractionated into saturates, aromatics, NSOs and asphaltenes. SOM and Total organic carbon (TOC) values reveal good generative potential of rocks. SOM and TOC values increase with depth which point out the increasing thermal maturity with depth. Bitumen to TOC ratio exhibits that samples are within the oil window. High API gravity, absence of unresolved complex mixture (UCM) and very low sulfur content indicate the non-biodegraded nature of the crude oils. The metals were present in a trace amount. This study provides scientific insight particularly for those involved in oil exploration in region under study.


https://doi.org/10.1007/s00248-019-01366-y

Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the “omics” technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.

Ngaba, M.J.Y., Hu, Y.-L., Bol, R., Ma, X.-Q., Jin, S.-F., Mgelwa, A.S., 2019. Effects of land use change from natural forest to plantation on C, N and natural abundance of 13C and 15N along a climate gradient in eastern China. Scientific Reports 9, 16516.

https://doi.org/10.1038/s41598-019-52959-z

Soil C and N turnover rates and contents are strongly influenced by climates (e.g., mean annual temperature MAT, and mean annual precipitation MAP) as well as human activities. However, the effects of converting natural forests to intensively human-managed plantations on soil carbon (C),

nitrogen (N) dynamics across various climatic zones are not well known. In this study, we evaluated C, N pool and natural abundances of δ13C and δ15N in forest floor layer and 1-meter depth mineral soils under natural forests (NF) and plantation forest (PF) at six sites in eastern China. Our results showed that forest floor had higher C contents and lower N contents in PF compared to NF, resulting in high forest floor C/N ratios and a decrease in the quality of organic materials in forest floor under plantations. In general, soil C, N contents and their isotope changed significantly in the forest floor and mineral soil after land use change (LUC). Soil δ13C was significantly enriched in forest floor after LUC while both δ13C and δ15N values were enriched in mineral soils. Linear and non-linear regressions were observed for MAP and MAT in soil C/N ratios and soil δ13C, in their changes with NF conversion to PF while soil δ15N values were positively correlated with MAT. Our findings implied that LUC alters soil C turnover and contents and MAP drive soil δ13C dynamic.

Ni, Z., Goracci, L., Cruciani, G., Fedorova, M., 2019. Computational solutions in redox lipidomics – Current strategies and future perspectives. Free Radical Biology and Medicine 144, 110-123.


The high chemical diversity of lipids allows them to perform multiple biological functions ranging from serving as structural building blocks of biological membranes to regulation of metabolism and signal transduction. In addition to the native lipidome, lipid species derived from enzymatic and non-enzymatic modifications (the epilipidome) make the overall picture even more complex, as their functions are still largely unknown. Oxidized lipids represent the fraction of epilipidome which has attracted high scientific attention due to their apparent involvement in the onset and development of numerous human disorders. Development of high-throughput analytical methods such as liquid chromatography coupled on-line to mass spectrometry provides the possibility to address epilipidome diversity in complex biological samples. However, the main bottleneck of redox lipidomics, the branch of lipidomics dealing with the characterization of oxidized lipids, remains the lack of optimal computational tools for robust, accurate and specific identification of already discovered and yet unknown modified lipids. Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics. Different levels of confidence for software assisted identification of redox lipidome are defined and necessary steps toward optimal computational solutions are proposed.

Nichols, J.E., Peteet, D.M., 2019. Rapid expansion of northern peatlands and doubled estimate of carbon storage. Nature Geoscience 12, 917-921.

https://doi.org/10.1038/s41561-019-0454-z

Northern peatlands are an integral part of the global carbon cycle—a strong sink of atmospheric carbon dioxide and source of methane. Increasing anthropogenic carbon dioxide and methane in the atmosphere are thought to strongly impact these environments, and yet, peatlands are not routinely included in Earth system models. Here we present a quantification of the sink and stock of northern peat carbon from the last glacial period through the pre-industrial period. Additional data and new algorithms for reconstructing the history of peat carbon accumulation and the timing of peatland initiation increased the estimate of total northern peat carbon stocks from 545 Gt to 1,055 Gt of carbon. Further, the post-glacial increases in peatland initiation rate and carbon accumulation

rate are more abrupt than previously reported. Peatlands have been a strong carbon sink throughout the Holocene, but the atmospheric partial pressure of carbon dioxide has been relatively stable over this period. While processes such as permafrost thaw and coral reef development probably contributed some additional carbon to the atmosphere, we suggest that deep ocean upwelling was the most important mechanism for balancing the peatland sink and maintaining the observed stability.



Significance: We report the discovery of a 50,000-y-old Neandertal tar-hafted flint tool found off the present-day Dutch coastline. The production of birch tar adhesives was a major technological development, demonstrating complex Neandertal technology and advanced cognitive ability. The rarity of Middle Paleolithic adhesive finds makes each new discovery crucial for improving our understanding of Neandertal lifeways. We demonstrate that birch tar was a routine part of the Neandertal technological repertoire. In addition, the complex know-how required for adhesive production in northwestern Europe during Marine Isotope Stage 4 and 3 was maintained in small groups leading highly mobile lives. This suggests a degree of task specialization and supports the hypothesis that ecological risk drives the development of complex technology.

Abstract: We report the discovery of a 50,000-y-old birch tar-hafted flint tool found off the present-day coastline of The Netherlands. The production of adhesives and multicomponent tools is considered complex technology and has a prominent place in discussions about the evolution of human behavior. This find provides evidence on the technological capabilities of Neandertals and illuminates the currently debated conditions under which these technologies could be maintained. 14C-accelerator mass spectrometry dating and the geological provenance of the artifact firmly associates it with a host of Middle Paleolithic stone tools and a Neandertal fossil. The find was analyzed using pyrolysis-gas chromatography-mass spectrometry, X-ray micro-computed tomography, and optical light microscopy. The object is a piece of birch tar, encompassing one-third of a flint flake. This find is from northwestern Europe and complements a small set of well-dated and chemically identified adhesives from Middle Paleolithic/Middle Stone Age contexts. Together with data from experiments and other Middle Paleolithic adhesives, it demonstrates that Neandertals mastered complex adhesive production strategies and composite tool use at the northern edge of their range. Thus, a large population size is not a necessary condition for complex behavior and technology. The mitigation of ecological risk, as demonstrated by the challenging conditions during Marine Isotope Stage 4 and 3, provides a better explanation for the transmission and maintenance of technological complexity.

Nozaki, T., Ohta, J., Noguchi, T., Sato, H., Ishikawa, A., Takaya, Y., Kimura, J.-I., Chang, Q., Shimada, K., Ishibashi, J.-i., Yasukawa, K., Kimoto, K., Iijima, K., Kato, Y., 2019. A Miocene impact ejecta layer in the pelagic Pacific Ocean. Scientific Reports 9, 16111.

https://doi.org/10.1038/s41598-019-52709-1

Meteorite impacts have caused catastrophic perturbations to the global environment and mass extinctions throughout the Earth’s history. Here, we present petrographic and geochemical evidence of a possible impact ejecta layer, dating from about 11 Ma, in deep-sea clayey sediment in the Northwest Pacific. This clay layer has high platinum group element (PGE) concentrations and features a conspicuous negative Os isotope anomaly (187Os/188Os as low as ~0.2), indicating an influx of extraterrestrial material. It also contains abundant spherules that include pseudomorphs suggestive of porphyritic olivine as well as spinel grains with euhedral, dendritic and spherical forms and NiO contents as great as 23.3 wt%, consistent with impact ejecta. Osmium isotope stratigraphy suggests a most plausible depositional age of ~11 Ma (Miocene) for this layer, as determined by fitting with the seawater evolution curve. No large impact crater of this age is known on land, even within the relatively large uncertainty range of the relative Os age. Thus, we suggest that an unrecognised impact event in the middle or late Miocene produced the impact ejecta layer of the Northwest Pacific.

Obata, D., Takabayashi, A., Tanaka, R., Tanaka, A., Ito, H., 2019. Horizontal transfer of promiscuous activity from nonphotosynthetic bacteria contributed to evolution of chlorophyll degradation pathway. Molecular Biology and Evolution 36, 2830-2841.


The relationship between enzymes and substrates does not perfectly match the “lock and key” model, because enzymes act on molecules other than their true substrate in different catalytic reactions. Such biologically nonfunctional reactions are called “promiscuous activities.” Promiscuous activities are apparently useless, but they can be an important starting point for enzyme evolution. It has been hypothesized that enzymes with low promiscuous activity will show enhanced promiscuous activity under selection pressure and become new specialists through gene duplication. Although this is the prevailing scenario, there are two major problems: 1) it would not apply to prokaryotes because horizontal gene transfer is more significant than gene duplication and 2) there is no direct evidence that promiscuous activity is low without selection pressure. We propose a new scenario including various levels of promiscuous activity throughout a clade and horizontal gene transfer. STAY-GREEN (SGR), a chlorophyll a—Mg dechelating enzyme, has homologous genes in bacteria lacking chlorophyll. We found that some bacterial SGR homologs have much higher Mg-dechelating activities than those of green plant SGRs, while others have no activity, indicating that the level of promiscuous activity varies. A phylogenetic analysis suggests that a bacterial SGR homolog with high dechelating activity was horizontally transferred to a photosynthetic eukaryote. Some SGR homologs acted on various chlorophyll molecules that are not used as substrates by green plant SGRs, indicating that SGR acquired substrate specificity after transfer to eukaryotes. We propose that horizontal transfer of high promiscuous activity is one process of new enzyme acquisition.

Ogwu, M.C., Srinivasan, S., Dong, K., Ramasamy, D., Waldman, B., Adams, J.M., 2019. Community ecology of Deinococcus in irradiated soil. Microbial Ecology 78, 855-872.

https://doi.org/10.1007/s00248-019-01343-5

Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of

gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct “radiation niches.” At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine–cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5–C12-containing compounds, like arabinose, lactose, N-acetyl-d-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.

Ok, S., Mal, T.K., 2019. NMR spectroscopy analysis of asphaltenes. Energy & Fuels 33, 10391-10414.


In crude oil production and processing, asphaltene aggregation followed by precipitation is a major problem for the oil industry as it causes deactivation of catalysts, blocking pipelines, and deposition on the internal surface of the reservoirs, etc. Asphaltenes, a complex mixture of a broad distribution of molecules, consisting of aromatic cores bonded to aliphatics and porphyrin type molecules with heavy metals, are defined based on solubility. Molecular complexity along with varying molecular weight distribution makes asphaltenes a difficult scientific problem to characterize. Over several decades, many researchers have contributed to characterization, analysis, and determination of structural properties of asphaltenes by various analytical techniques. Nuclear magnetic resonance (NMR) spectroscopy and relaxometry are widely applied for characterizing the chemical structures of asphaltenes, interactions between asphaltenes and maltenes, and dynamical behaviors of asphaltenes in bulk and in confined states. The goal of the current review article is to give an insight into various aspects of asphaltene analysis by NMR spectroscopy and relaxometry. Following a short introduction on asphaltenes and theory of NMR technique, recent contributions on asphaltenes by NMR techniques are summarized and presented. Lessons learned and suggestions on possible future work conclude the present review article.

Ooki, A., Shida, R., Otsu, M., Onishi, H., Kobayashi, N., Iida, T., Nomura, D., Suzuki, K., Yamaoka, H., Takatsu, T., 2019. Isoprene production in seawater of Funka Bay, Hokkaido, Japan. Journal of Oceanography 75, 485-501.

https://doi.org/10.1007/s10872-019-00517-6

We carried out shipboard observations in Funka Bay, Hokkaido, Japan, monthly or bimonthly from December 2015 to November 2016. We measured vertical profiles of isoprene, chlorophyll-a (chl-a), and other parameters from surface to bottom layer (about 95 m) near the center of the bay. We found substantial increases in isoprene concentration in the surface mixed layer from February to March during the peak of the spring diatom bloom, in the bottom layer from March to April after the peak of the bloom, and in the subsurface layer (below the surface mixed layer) in summer from July to August, where there were also substantial chl-a concentration maxima. We attribute the increased isoprene in the surface and subsurface layers to photosynthetic production of isoprene by the dominant phytoplankton in the spring bloom and in summer, and that in the bottom layer to dark production of isoprene by diatom aggregates that settled from the surface euphotic zone. We also measured isoprene production in laboratory incubation experiments. The rates of in situ production of isoprene per unit chl-a in the surface mixed layer during the spring bloom, in the dark bottom layer during the bloom, and in the subsurface layer in summer (0.82, 0.03–0.13, and 7.38 pmol (μg chl-a)−1 day−1, respectively) were consistent with our incubation results. We believe that this is the first report focused on dark production of isoprene by diatoms; the rate of isoprene production under dark conditions ranged from 4% to 16% of that by photosynthesis.



We investigated the sediment properties and gas hydrate saturations in pressure-cores recovered during the National Gas Hydrate Program Expedition 02 (NGHP-02) in Areas B, C, and E of the Krishna–Godavari Basin (K–G Basin) off the eastern margin of India. These investigations included the analyses of grain size, mineralogy, and grain density and employed scanning electron microscopy (SEM). Sediments with median grain sizes below 90 μm were generally observed within most of the pressure-cores, whereas sediments with median grain sizes exceeding 250 μm were only observed in a few pressure-cores. Higher concentrations of gas hydrate were found in sediment layers with median grain sizes of 10–90 μm; the occurrence of gas hydrates was lower in sediment layers with median grain sizes below 10 μm. Three types of gas hydrate-bearing sediments containing above 50 vol.% gas hydrate saturations were observed: (1) sediments with silt grain size ratios above 70 vol.%, (2) sediments with sand grain size ratios above 35 vol.%, and (3) coarser sandy sediments with gravel. Sandy sediments with high gas hydrate saturations (above 50 vol.%) were very minor constituents in the pressure-core sediments. The gas hydrate saturations were lower in sediments with a clay fraction above 30 vol.%. SEM images revealed microfossil debris, fragments of sedimentary rock, and silt/sand-sized-agglomerated grains throughout the pressure-cores, which indicate that the sediments were deposited at and/or transported to the foot of the continental slope through reworking of upper-slope deposits. The geological setting and SEM observations indicate that the pressure-core sediments are mainly a terrigenous source, with a small component from pelagic or hemipelagic sedimentation. The results of the pressure-core analyses confirm that natural gas hydrates can occur in silt-rich sediments. The occurrence of gas hydrates in the pressure-core sediments recovered during the NGHP-02 is controlled by the lithology of the sediments, especially their clay content.

Ostrander, C.M., Kendall, B., Olson, S.L., Lyons, T.W., Gordon, G.W., Romaniello, S.J., Zheng, W., Reinhard, C.T., Roy, M., Anbar, A.D., 2020. An expanded shale δ98Mo record permits recurrent shallow marine oxygenation during the Neoarchean. Chemical Geology 532, 119391.


Multiple attempts have been made using the ancient shale record to track the molybdenum isotope composition (δ98Mo) of seawater during the final two-hundred million years of the Archean Eon (2.7 to 2.5 billion-years-ago, or Ga). This seawater δ98Mo value is important because it should have scaled with levels of ocean oxygenation during the runup to the Great Oxidation Event (GOE). Unfortunately, however, it is difficult to tell if the majority of the existing late-Archean shale δ98Mo record tracks an ancient seawater value. Here, we further attempt to track pre-GOE seawater δ98Mo using an expanded and well-characterized shale sample set from Western Australia (Jeerinah, Wittenoom, and Mt. Sylvia formations) and South Africa (Nauga and Klein Naute formations). Most importantly, and in contrast to most previous Mo isotope studies of similarly aged shales, local redox conditions for our shales have been independently constrained using the iron (Fe) speciation proxy and bottom-water Mo contents at the time of deposition have been qualitatively estimated using Mo/TOC ratios. Local redox conditions and bottom water Mo availability are important parameters because transfer of the seawater δ98Mo to sediments today is shown to be dependent on these conditions. According to our updated sedimentary δ98Mo record, seawater δ98Mo commonly exceeded 1.0‰ between ~2.69 Ga and 2.50 Ga. In order to drive such a heavy seawater δ98Mo, there must have been a marine sink with a strong preference for lighter-mass Mo isotopes frequently present over this timeframe. The operation of some anaerobic processes in late-Archean marine settings could theoretically explain the heavier seawater δ98Mo. Such processes are known to promote the preferential retention of lighter-mass Mo isotopes in marine sediments today (e.g., interactions between Mo and organic matter or the formation of thio-complexes). Alternatively, or in addition, adsorption of lighter-mass Mo isotopes to Fe and Mn oxide minerals formed in oxygenated marine environments can explain the heavier seawater δ98Mo. A compilation of previous work suggests that oxygenated shallow marine environments were fairly common during the late-Archean, and thus Mo adsorption to FeMn oxides formed in these settings probably played an important role in driving heavy seawater δ98Mo over this timeframe.

Overall, K.L., Dunham, A.E., Scheifele, P., Sonstrom Malowski, K., 2019. Fear of noises affects canine problem solving behavior and locomotion in standardized cognitive tests. Applied Animal Behaviour Science 221, 104863.


As part of a larger problem solving study, 22 dogs who were identified by owners/clients as reacting to noise and 13 identified by owners/clients as not reacting to noise that had been previously compared for auditory function were compared with respect to their reported noise reactions, performance on a puzzle box test, response to a provocative noise recording, and movement. Each dog was evaluated using a standardized, validated, semi-quantitative objective questionnaire from which an Anxiety Intensity Rank (AIR) score was calculated. AIR score calculations reflect the number of categories of noise to which the dog reacts, the behaviors exhibited, and the intensity of the reaction. Each dog underwent a 13 item problem-solving test (The Canine Intelligence Test Protocol; CITP) designed to evaluate 4 standardly evaluated cognitive domains. We report on two of the 13 tests – the puzzle box test and the provocative noise test – for this group of dogs. During testing

most dogs wore collars containing accelerometers using custom firmware which provided second-by-second 3D movement data. AIR scores for the 2 groups differed significantly (Welch’s t tests; t = 4.34, df = 19.23, P < 0.0004), although the affected group was only mildly affected. Affected dogs took longer to solve the tasks and, overall, did more poorly (P < 0.5). Accelerometry revealed that during testing, movements of affected dogs were more erratic, less continuous and subject to greater extreme deviations and longer pauses than were the movements of unaffected dogs. Even dogs mildly affected with fear of noises differed from unaffected dogs, and performed more poorly on problem-solving tests possibly, in part, because their movements were characterized by a high degree of physical and behavioral/emotional reactivity. Reactions to noise affect how these dogs move, which may affect every investigatory and interactive aspect of their lives. Combining AIR scores with movement measures may be a useful method to assess welfare in pet dogs.

Palacios, P.A., Snoeyenbos-West, O., Löscher, C.R., Thamdrup, B., Rotaru, A.-E., 2019. Baltic Sea methanogens compete with acetogens for electrons from metallic iron. The ISME Journal 13, 3011-3023.

https://doi.org/10.1038/s41396-019-0490-0

Microbially induced corrosion of metallic iron (Fe0)-containing structures is an environmental and economic hazard. Methanogens are abundant in low-sulfide environments and yet their specific role in Fe0 corrosion is poorly understood. In this study, Sporomusa and Methanosarcina dominated enrichments from Baltic Sea methanogenic sediments that were established with Fe0 as the sole electron donor and CO2 as the electron acceptor. The Baltic-Sporomusa was phylogenetically affiliated to the electroactive acetogen S. silvacetica. Baltic-Sporomusa adjusted rapidly to growth on H2. On Fe0, spent filtrate enhanced growth of this acetogen suggesting that it was using endogenous enzymes to retrieve electrons and produce acetate. Previous studies have proposed that acetate produced by acetogens can feed commensal acetoclastic methanogens such as Methanosarcina. However, Baltic-methanogens could not generate methane from acetate, plus the decrease or absence of acetogens stimulated their growth. The decrease in numbers of Sporomusa was concurrent with an upsurge in Methanosarcina and increased methane production, suggesting that methanogens compete with acetogens for electrons from Fe0. Furthermore, Baltic-methanogens were unable to use H2 (1.5 atm) for methanogenesis and were inhibited by spent filtrate additions, indicating that enzymatically produced H2 is not a favorable electron donor. We hypothesize that Baltic-methanogens retrieve electrons from Fe0 via a yet enigmatic direct electron uptake mechanism.

Pan, N., Li, D., Lü, W., Dai, F., 2019. Kinetic study on the pyrolysis behavior of Jimsar oil shale Oil Shale 36, 462–482.

https://doi.org/10.3176/oil.2019.4.02

It is well known that the process of oil shale pyrolysis is extremely complicated, for several competing or parallel reactions occur simultaneously, and various products are continuously generated, serving as new reactants. In this work, it is assumed that there occur two parallel reactions in the devolatilization of organic matter, one represents the volatilization of bitumen and the other represents the pyrolysis of kerogen. Kinetic triplets for the competing or parallel reactions are different from each other. To investigate the pyrolysis mechanism of Jimsar oil shale of Xinjiang

Province, China in more detail, the bi-Gaussian distribution method, a multi-stage parallel reaction model and two master plots methods are adopted to determine the kinetic models in this work. The apparent activation energy (E) is calculated by the Flynn-Wall-Ozawa (F-W-O), Kissinger-Akahira-Sunose (K-A-S) and Friedman methods. According to the results, it can be concluded that heating rate exerts little influence on the kinetic parameters but has some impact on the pyrolysis process as a whole. The results of this work reveal the pyrolysis characteristics of oil shale to a certain extent.

Pan, S., Wang, Q., Bai, J., Liu, H., Chi, M., Cui, D., Xu, F., 2019. Investigation of behavior of sulfur in oil fractions during oil shale pyrolysis. Energy & Fuels 33, 10622-10637.


In this study, the theoretical and experimental basis for the examination of sulfur-containing compounds during the pyrolysis of oil shale, involving 19 sulfur compound models and 34 corresponding reaction pathways, is discussed. In addition, the types of sulfur compounds in shale oils at different pyrolysis temperatures were determined by flash pyrolysis–gas chromatography–mass spectrometry and a gas chromatography–sulfur chemiluminescence detector. The reaction pathway for the sulfur-containing model provided reliable results for the conversion behavior of sulfur, which was consistent with the experimental values. With increasing temperature, the content of Cn-thiophene continuously decreased. In contrast, the Cn-benzothiophene concentration generally increased with increasing temperature. The S═O double bond affected the C–S bond order, and the bond order was reduced due to the effect of oxygen atoms. Calculation results revealed that the alkyl side-chain group tends to form an aromatic ring structure, leading to the increase in the relative content of Cn-thiophene/benzothiophene. Meanwhile, the Mulliken atomic charge, bond dissociation energy, bond length, and Mayer bond order of thioether and sulfoxide compounds were estimated. Quantum chemistry was successfully employed to analyze the chemical reactions, which provided a basis for promoting the understanding of the kerogen pyrolysis mechanism at the molecular level.

Pančić, M., Köhler, E., Paulsen, M.L., Toxværd, K., Lacroix, C., Le Floch, S., Hjorth, M., Nielsen, T.G., 2019. Effects of oil spill response technologies on marine microorganisms in the high Arctic. Marine Environmental Research 151, 104785.


We studied how exposure to oil spill response technologies affect marine microorganisms during Arctic winter and spring. Microorganisms were exposed to chemically dispersed oil (DISP), in situ burnt oil (ISB), and natural attenuated oil (NATT) in mesocosms from February to May. We subsampled the mesocosms and studied the effects of oil in laboratory incubations as changes in biomass of the major functional groups: bacteria, heterotrophic-nanoflagellates, dinoflagellates, ciliates, pico- and nanophytoplankton, and diatoms over two 14-day periods. In winter, the majority of polycyclic aromatic hydrocarbons (PAHs) remained encapsulated in the ice, and the low concentrations of PAHs in water led to minute changes in biomass of the investigated groups. In spring, however, when the PAHs were partially released from the melting ice, the biomass of many functional groups in DISP and NATT decreased significantly, while the changes in ISB were less pronounced. The overall biomass reduction, as observed in this study, could lead to a disrupted transfer of energy from the primary producers to the higher trophic levels in oil affected areas.

Pandey, L., Sain, K., Joshi, A.K., 2019. Estimate of gas hydrate saturations in the Krishna-Godavari basin, eastern continental margin of India, results of expedition NGHP-02. Marine and Petroleum Geology 108, 581-594.


A total of 25 drill sites were established in the Krishna-Godavari (KG) and Mahanadi Basins along the eastern margin of India during the India National Gas Hydrate Program Expedition 02 (NGHP-02) with the goal to identify and characterize gas hydrate occurrences in sand-rich reservoir systems. The objective of this study is to characterize the gas hydrate bearing zones linked with two seismic inferred horizons (R1 and R2) and estimate gas hydrate saturations at two sites in Area B of the KG Basin: Sites NGHP-02-22 and NGHP-02-23. The upper seismic-imaged reservoir section (reflector R1) contains both pore-filling and fracture-filling gas hydrate, while the lower seismic-imaged reservoir section (reflector R2) has only pore-filling gas hydrate. Since electrical resistivity seems to be the most pronounced physical response to the presence of gas hydrate, we have analyzed the resistivity log data using Archie's empirical equation from two sites based on an isotropic reservoir model. In order to assess the gas hydrate saturation, we have also performed isotropic velocity modelling using the three-phase Biot equation (TPBE) and density log derived sediment porosities. At Site NGHP-02-22, the average gas hydrate saturation estimated using the resistivity log data and P-wave velocity modelling are 29% and 17%, respectively in the depth interval of 207–290 mbsf whereas at Site NGHP-02-23, the average gas hydrate saturation obtained from resistivity log data and P-wave velocity modelling are 25% and 60%, respectively in the depth interval of 271–288 mbsf. Estimated results are further validated with the pressure core derived gas hydrate saturations to ensure their reliability at the respective drill sites. It was found that P-wave velocity log-inferred gas hydrates show a slight mismatch with the pressure core derived hydrate saturations while, the electrical resistivity log based result depicts a major mismatch with the pressure core derived hydrate saturations. The reason for this discrepancy is likely due to isotropic resistivity analysis of the reservoir section having anisotropic properties.



The secondary migration mechanism, enrichment factors of Jurassic tight oil in central Sichuan Basin were well investigated through physical simulation experiment of reservoir formation, casting and fluorescent thin sections, field emission scanning electron microscope (FESEM) and environment scanning electron microscope (ESEM). The results show that migration of Jurassic tight oil in central Sichuan Basin is a low-velocity non-Darcy flow through low-efficient migration path under the huge migration driving force, and has three migration and seepage stages, i.e. viscous flow stage, nonlinear seepage stage, and quasi-liner seepage stage. Microscopically, the migration pathway of tight oil is the pore-fracture composite conduction; macroscopically, the migration mode of tight oil is the large-scale short–distance migration. Distribution of favorable zones of tight oil is controlled by distribution of high-quality source rocks. The hydrocarbon-generation strength of 0.4 × 106 t/km2 can be as a threshold to determine favorable zone of tight oil in the study area. The reservoirs with

high permeability and high porosity can form tight oil sweet spots, and the development degree of fractures is closely related to well with high yield of tight oil well.



A p-cresol degrading bacterial strain was isolated from coke oven wastewater of an iron and steel plant industry. The isolated strain was identified as Pseudomonas citronellolis NS1 by 16S rRNA gene sequencing method. The isolated Pseudomonas species could degrade 1200 mg l−1 of p-cresol completely in 40 h. Further, at 1200 mg l−1 of initial p-cresol more than 95.4% TOC and 98.5% toxicity removal were also achieved by the microbial culture. The metabolic pathway of the Pseudomonas species was investigated using HPLC, UV visible spectra, FT-IR and GC–MS analysis. The major metabolic intermediate products identified in the bacterial culture were 4-methyl catechol, protocatechuic acid, 3-oxadipic acid, 4- carboxy muconolactone, 2-hydroxy muconicsemialdehyde and maleic acid. Based on the identified metabolic intermediate products, a tentative new meta-cleavage 3-oxoadipate pathway has been proposed. The biodegradation of p-cresol by the culture followed first order kinetic. The biokinetic parameters associated with biodegradation of p-cresol have been estimated as follow; μ = 0.353 h−1, Ksi = 464 mg l−1, Ks = 99.5 mg l−1. It was observed that, when the initial concentrations of p-cresol exceeded more than 1000 mg l−1, about 70% of the total substrate carbon was utilized towards microbial maintenance energy.

Paul, S., Gross, D., Bechtel, A., Dutta, S., 2020. Preservation of monoterpenoids in Oligocene resin: Insights into the evolution of chemical defense mechanism of plants in deep-time. International Journal of Coal Geology 217, 103326.


Monoterpenoid class of compounds is well-known for the characteristic odor and their contribution in various ecological functions such as plant-insect interaction, defense, pollinator attraction etc. They are extremely volatile and labile by nature and therefore their preservation in geological samples is quite uncommon. In the present article we report, exceptionally preserved monoterpenoids in late Oligocene resin from offshore Shimokita, Japan. Compounds viz. fenchol, fenchone, camphor, borneol, isoborneol are detected in appreciable quantity while camphene, isocamphene and p-cymene are found in low amount. Such rare phenomenon suggests that the amber must have experienced some unique diagenetic condition which favored the preservation of these volatile compounds. These monoterpenes have distinct aroma and they actively contribute into the chemical defense mechanisms of extant plant species. Their excellent preservation in late Oligocene amber depicts that such chemical defense strategies had already been developed by plants during early Cenozoic.

Paula-Santos, G.M., Caetano-Filho, S., Enzweiler, J., Navarro, M.S., Babinski, M., Guacaneme, C., Kuchenbecker, M., Reis, H., Trindade, R.I.F., 2020. Rare earth elements in the terminal Ediacaran

Bambuí Group carbonate rocks (Brazil): evidence for high seawater alkalinity during rise of early animals. Precambrian Research 336, 105506.


Rare earth elements plus yttrium (REY) mass fractions of ancient carbonate rocks are used to track changes in chemistry of past seawater. Here we investigate REY patterns in two carbonate sections from the Ediacaran Bambuí Group, São Francisco Basin (Brazil), which comprise its two lowermost transgressive-regressive second-order sedimentary sequences. Shale normalised distributions vary with the sequence stratigraphy framework. In the basal 2nd-order sequence, carbonate samples from the basal sequence transgressive systems tract display light REY (LREY) distributions slightly depleted to enriched that reflect input of freshwater, possibly in a post glacial episode. Upwards, carbonate rocks from the early highstand systems tract (EHST) yielded LREY enriched distributions, which progressively turns into LREY shale normalized depleted distributions on samples from the late highstand systems tract (LHST). This portion of the sequence also displays Y positive anomaly in some cases. Carbonate samples from the upper second-order sequence do not display coherent patterns. Ce/Ce* values > 1 in most samples throughout the two sections suggest permanent anoxia of seawater. The REY change from the EHST to LHST in the basal sequence marks an important paleoenvironmental overturn in the basin, with increasing alkalinity in seawater driving REY fractionation and LREY depletion. Confinement of the basin in the inner areas of West Gondwana due the uplift of marginal neoproterozoic orogens probably changed the weathering style of source areas to more congruent, thus delivering a higher ionic influx to a restricted setting, increasing alkalinity during LHST. Cloudina sp. fragments were reported in this stage of the Bambuí Group and in carbonate rocks with high Sr mass fractions in other West Gondwana basins, supporting the hypothesis that the high alkalinity of seawater during late Ediacaran may have driven the appearance of the first biomineralizing organisms.

Pearson, A., 2019. Resolving a piece of the archaeal lipid puzzle. Proceedings of the National Academy of Sciences 116, 22423-22425.

http://www.pnas.org/content/116/45/22423.abstract

Lipid membranes are common to all cells, despite occurring in many different forms across Earth’s great biotic diversity. Among the most distinctive membranes are those formed by the archaea, whose lipids are characterized by sn-2,3-glycerol stereochemistry (in contrast to sn-1,2-glycerol in bacteria and eukarya), isoprenoid rather than acetyl hydrophobic chains, and frequent occurrence as membrane-spanning macrocycle structures (1). The membrane-spanning lipids consist of mixed assemblages of structural isomers containing up to 8 internal cyclopentane rings (GDGT-0 through GDGT-8 [glycerol dibiphytanyl glycerol tetraethers with zero to 8 rings]) (Fig. 1). Many aspects of the biosynthesis of these unusual structures remain unknown, but, in PNAS, Zeng et al. (2) take an important step forward by revealing genes encoding for 2 enzymes involved in synthesis of the cyclopentane moieties. Pinpointing these genes is critical not only for understanding archaeal biosynthetic pathways but also for resolving questions about the primary sources of the GDGTs that are widely detected in the environment.Fig. 1. (A) GDGTs containing cyclopentane rings are widely distributed among the archaea. (B) GDGTs are membrane-spanning tetraether lipids with 2 C40 isoprenoid chains (R, R’), each containing zero to 4 cyclopentane rings (and sometimes a cyclohexane ring, not shown). Tetraethers are formed from the diether precursor, DGGGP, in which the phosphate is replaced by an alternative polar group (X) before tetraether formation. (C) The

sequence of biosynthetic steps leading from 2×[DGGGP] → GDGT remains unknown, but a plausible order would be tetraether synthesis using an MSS, a step that requires the Δ14-15 double bond (22); GrsA and GrsB in sequence, as shown by Zeng et al. (2); and final saturation



Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had “young” sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.

Peñalver, R., Arroyo-Manzanares, N., López-García, I., Hernández-Córdoba, M., 2020. An overview of microplastics characterization by thermal analysis. Chemosphere 242, 125170.


Microplastics may be present in the environment as primary microplastics (manufactured) or secondary microplastics (result of the continuous degradation of larger plastic pieces into smaller fragments due to environmental, physicochemical and biotic factors). To fully understand the dynamics of microplastic particles and their environmental effects, harmonized, automated, cheap, rapid and reliable methodologies for sampling, extraction and characterization of microplastic need to be developed. This review focuses on the potential of thermal analytical techniques for microplastics characterization and highlights some of the new trends in this area.

Peng, S., Ren, B., Meng, M., 2019. Quantifying the influence of fractures for more-accurate laboratory measurement of shale matrix permeability using a modified gas-expansion method. SPE Reservoir Evaluation & Engineering 22, 1293-1304.

https://doi.org/10.2118/195570-PA

Matrix permeability is a key petrophysical parameter in reservoir evaluation and simulation. However, measurement of this parameter remains problematic for unconventional reservoirs. One of the challenges lies in the influence of fractures. Inclusion of fractures can lead to overestimation of shale matrix permeability. In this paper, new experimental and data-analysis procedures are developed for more-accurate yet relatively fast measurement of shale matrix permeability on the basis of previous work (Peng and Loucks 2016). The influence of fractures on matrix porosity and permeability is quantified and excluded. Reliability and consistency of the measurement results are confirmed through multiple means, including analytical solution back calculation and measurements for similar samples but with different plug diameters. Because the influence of fractures is explicitly excluded in data analysis, the new method is also more flexible regarding sample conditions—even broken plug samples with fractures can be used in this method. This is another advantage of the new method given the difficulty in obtaining “intact” plugs because of the fissility of shale.

Penny, A., Kröger, B., 2019. Impacts of spatial and environmental differentiation on early Palaeozoic marine biodiversity. Nature Ecology & Evolution 3, 1655-1660.

https://doi.org/10.1038/s41559-019-1035-7

The unprecedented diversifications in the fossil record of the early Palaeozoic (541–419 million years ago) increased both within-sample (α) and global (γ) diversity, generating considerable ecological complexity. Faunal difference (β diversity), including spatial heterogeneity, is thought to have played a major role in early Palaeozoic marine diversification, although α diversity is the major determinant of γ diversity through the Phanerozoic. Drivers for this Phanerozoic shift from β to α diversity are not yet resolved. Here, we evaluate the impacts of environmental and faunal heterogeneity on diversity patterns using a global spatial grid. We present early Palaeozoic genus-level α, β and γ diversity curves for molluscs, brachiopods, trilobites and echinoderms and compare them with measures of spatial lithological heterogeneity, which is our proxy for environmental heterogeneity. We find that α and β diversity are associated with increased lithological heterogeneity, and that β diversity declines over time while α increases. We suggest that the enhanced dispersal of marine taxa from the Middle Ordovician onwards facilitated increases in α diversity by encouraging the occupation of narrow niches and increasing the prevalence of transient species, simultaneously reducing spatial β diversity. This may have contributed to a shift from β to α diversity as the major determinant of γ diversity increase over this critical evolutionary interval.

Percival, L.M.E., Bond, D.P.G., Rakociński, M., Marynowski, L., Hood, A.v.S., Adatte, T., Spangenberg, J.E., Föllmi, K.B., 2020. Phosphorus-cycle disturbances during the Late Devonian anoxic events. Global and Planetary Change 184, 103070.


The Late Devonian was marked by repeated faunal crises and episodes of geographically widespread marine anoxia, and featured one of the ‘Big Five’ mass extinctions of the Phanerozoic Aeon during

the Frasnian–Famennian transition. However, the processes responsible for causing the numerous anoxic events remain unclear. This study highlights the occurrence of disturbances to the phosphorus cycle during several Late Devonian crises by investigating sedimentary concentrations of the element (Ptot) as a tracer of nutrient influx, as well as its ratio with total organic carbon (TOC) to infer the recycling of the element from marine sediments. Increased TOC/P tot ratios in the Frasnian–Famennian Lower and Upper Kellwasser horizons and upper Famennian Annulata and Hangenberg levels suggest that such nutrient recycling occurred across extensive areas of the marine shelf in Laurentia and both Rheic Ocean margins at those times, helping to sustain reducing conditions in those environments. Elevated Ptot values in the Upper Kellwasser, Annulata, and Hangenberg levels are consistent with an enhanced nutrient influx as the initial trigger for the anoxia. Correlation of phosphorus trends with other geochemical indicators of weathering/detrital influx (osmium-isotope, silicon/aluminum, and titanium/aluminium ratios) support a scenario in which terrestrial runoff provided these nutrients both to marine shelves and the oceanic inventory. Upwelling of oceanic deep-water bodies may have then brought the phosphorus to areas that had not featured major direct inputs of terrigenous material. The exception is the Lower Kellwasser Event, during which there was no increase in phosphorus delivery to marine areas and no evidence for terrestrial influx at the studied sections, invoking a different mechanism for the development of water-column anoxia. Clearly, the Late Devonian marine realm was unusually susceptible to becoming anoxic through various possible triggers, including nutrient influx from land and/or deep-water upwelling, and the recycling of phosphorus from newly deposited sediments.



An amber (UFRPE 5037), from the black shales of the Ipubi Formation, Araripe Basin (Brazil), has been analyzed to understand its organic geochemical characteristics and possible botanical source using gas chromatography–mass spectrometry (GC–MS). The analyses carried out detected monoterpenes, hydrocarbonic sesquiterpenes, and aliphatic diterpanes like abietanes and norabietanes, as well as aromatic diterpanes such as simonellite, norsimonellite, retene, hinokiol, ferruginol and dehydroabietic acid. Such a combination of components is mainly known to have originated from gymnosperms. The individual identification of diterpenoids allowed the suggestion of Cheirolepidiaceae or Podocarpaceae families as possible amber producers, pointing to a flora similar to the underlying Crato Formation. Therefore, UFRPE 5037 consists on the first amber record in the Ipubi Formation, allowing the acquisition of important information regarding the botanical sources associated to new Brazilian amber occurrence described here.

Perini, N., Mercuri, F., Thaller, M.C., Orlanducci, S., Castiello, D., Talarico, V., Migliore, L., 2019. The stain of the original salt: Red heats on chrome tanned leathers and purple spots on ancient parchments are two sides of the same ecological coin. Frontiers in Microbiology 10, 2459. doi: 10.3389/fmicb.2019.02459.


Animal hides are one of man’s earliest and mostly used materials; many rawhide products, primarily leather, have for centuries been used for several purposes. The peculiar mechanical properties of leather depend on the hide composition, a dense collagen feltwork. Unfortunately, due to their proteic composition, rawhides may undergo microbial attack and biodeterioration. Over centuries, different processes and treatments (brining, vegetal or chrome tanning, tawing, etc.) were set up to face the biological attack and modify/stabilise the hide’s mechanical properties. Nevertheless, even present-day rawhides are subjected to biological colonisation, and traces of this colonisation are clearly shown in Chrome(III) tanned leathers (in the wet blue stage), with obvious economic damages. The colonisation traces on tanned leathers consist of isolated or coalescent red patches, known as red heat deterioration. Parchments are rawhide products, too; they derive from another manufacturing procedure. Even parchments undergo microbial attack; the parchment biodeterioration seems comparable to leather red heat deterioration and is known as purple spots. Recently, an ecological succession model explained the process of historical parchment purple spot deterioration; the haloarchaea Halobacterium salinarum is the pioneer organism triggering this attack. The marine salt used to prevent rawhide rotting is the carrier of haloarchaea colonisers (Migliore et al., 2019). The aim of this study was to investigate the dynamics of biodeterioration on Chrome(III) tanned leathers and its effects on the stability/integrity of collagen structure. To this end, standard cultivation methods were integrated with three updated technologies, Next-Generation Sequencing (NGS), Raman spectroscopy, and Light Transmitted Analysis (LTA). A bioinformatic comparison between chrome tanned leather vs. historical parchment colonisers was performed to evaluate if leather and parchment share common culprits; furthermore, the effect of the biodeterioration on the physical properties of the hide product was evaluated.

Peter, K.T., Wu, C., Tian, Z., Kolodziej, E.P., 2019. Application of nontarget high resolution mass spectrometry data to quantitative source apportionment. Environmental Science & Technology 53, 12257-12268.


High resolution mass spectrometry (HRMS) analyses provide expansive chemical characterizations of environmental samples. To date, most research efforts have developed tools to expedite labor- and time-intensive contaminant identification efforts. However, even without chemical identity, the richness of nontarget HRMS data sets represents a significant opportunity to chemically differentiate samples and delineate source contributions. To develop this potential, we evaluated the use of unidentified HRMS detections to define sample uniqueness and provide additional statistical resolution for quantitative source apportionment, overcoming a critical limitation of existing approaches based on targeted contaminants. By creating a series of sample mixtures that mimic pollution sources in a representative watershed, we assessed the fidelity of HRMS source fingerprints during dilution and mixing. This approach isolated 8–447 nontarget compounds per sample for source apportionment and yielded accurate source concentration estimates (between 0.82 and 1.4-fold of actual values), even in multisource systems with <1% source contributions. Furthermore, we mined the nontarget data to identify five source-specific chemical end-members amenable to apportionment. While additional development studies are needed to fully evaluate the myriad factors affecting method accuracy and capabilities, this study provides a conceptual foundation for novel applications of nontarget HRMS data to confidently distinguish and quantify source impacts in complex systems.

Philp, R.P., DeGarmo, C.D., 2020. Geochemical characterization of the Devonian-Mississippian Woodford Shale from the McAlister Cemetery Quarry, Criner Hills Uplift, Ardmore Basin, Oklahoma. Marine and Petroleum Geology 112, 104078.


It has been estimated that technically recoverable reserves from shales in the continental U.S. are believed to be approximately 24 billion barrels of oil (BBO) and 750 trillion cubic feet (Tcf) of gas. In Oklahoma the most important hydrocarbon source rock is the Woodford Shale, proposed to be the source of some 70% of the state's liquid hydrocarbon reserves. Such a regionally widespread source rock provides potential for both academic study and industrial opportunities. In this study representative samples of the Woodford Shale from the McAlister Quarry outcrop have been characterized by a variety of geochemical techniques. TOC values range from 0.07 to 15.6 wt% and, based on Rock-Eval Pyrolysis, most of the samples plot within the Type I/II kerogen range, with several low TOC samples plotting in the Type III kerogen range. TOC and biomarker parameters, suggests that two sections of the Upper Woodford are immature paleosols, having been subaerially exposed due to abrupt episodes of sea level fall during the Late Devonian. Evidence for these zones of paleoweathering includes highly depleted TOC, increased oxygen index (OI) values, loss of n-alkanes, decreases in the aryl isoprenoid ratio (AIR), sesquiterpenoids, cheilanthanes, hopanoids, and decreases in many of the polycyclic aromatic hydrocarbons (PAHs).

The values of several paleoenvironmental proxies for samples immediately following the Frasnian-Famennian (F–F) Stage extinction boundary within the Upper Woodford suggests that a large influx of weathered terrigenous material occurred at that time. The presence of pyrogenic compounds implies that paleowildfires were widespread throughout the Middle and Late Devonian in the North American midcontinent. It is possible that these influxes of weathered terrestrial organic material stimulated algal blooms that led to the anoxic water column conditions often attributed to the F–F Stage extinction event. Investigation of the stratigraphic framework of these source rocks assists in evaluating their potential as hydrocarbon producers and/or unconventional reservoirs. Integration of geochemical data adds another powerful dimension to this approach.

It has been proposed that the Woodford Shale was deposited during a 2nd order depositional sequence. The lower member represented the transgressive systems tract (TST), the Upper member the highstand systems tract (HST), and the Middle member bridging the transition between the two. Numerous 3rd order parasequences were also identified as being part of the overall 2nd order sequence and could be correlated to the Devonian sea level curve.

The major objectives of the study were:

While this study focuses locally on the McAlister Quarry samples, it is also of regional importance. The Woodford is a prolific source rock throughout the Anadarko Basin and has been the subject of extensive exploration and production efforts, particularly in the past decade with the development of horizontal drilling and hydrofracturing techniques. Continued investigation of the heterogeneity of the shale will greatly enhance the ability to predict more productive facies within the formation throughout the basin.



The burial of organic carbon (OC) in sedimentary environments promotes long-term carbon sequestration, which allows the release of oxygen in the atmosphere. Organo-mineral interactions that form between terrigenous minerals and OC during transport to and deposition on the seabed enhance OC preservation. Here, we propose an authigenic mechanism for the coupled preservation of labile OC and metastable iron sulfide minerals under anoxic conditions. Sulfate-reducing microorganisms (SRM) are ubiquitous in anoxic environments and produce the majority of free sulfide in marine sediments, leading to the formation of iron sulfide minerals in situ. Using high spatial resolution microscopy, spectroscopy and spectro-microscopy, we show that iron sulfide biominerals precipitated in the presence of SRM incorporate and adsorb organic molecules, leading to the formation of stable organo-mineral aggregates that could persist for years in anoxic environments. OC/iron sulfide assemblages consist of the metastable iron sulfide mineral phases mackinawite and/or greigite, along with labile organic compounds derived from microbial biomass or from organic molecules released extracellularly by SRM. Together these results underscore the role that a major group of anoxic microbes play in OC preservation and illustrate the value of the resulting authigenic metastable iron sulfide minerals mackinawite and greigite in protecting labile organic molecules from degradation over time.

Piedrahita, J., Aguilera, R., 2019. Geochemical Productivity Index (Igp): An innovative way to identify potential zones with moveable oil in shale reservoirs. SPE Reservoir Evaluation & Engineering 22, 1256-1264.

https://doi.org/10.2118/191644-PA

In this paper we present a method for identifying intervals in shale oil reservoirs that contain moveable hydrocarbons with a novel geochemical productivity index (PI), Igp. This index merges three important rock properties that must always be considered for sound shale oil reservoir characterization: vitrinite reflectance (%Ro), oil-saturation index (OSI), and free-water porosity (φFW). Integrating this index with other petrophysical properties and geomechanical parameters defines intervals with high moveable oil content.

Shale oil is both a source rock and an unconventional reservoir rock. Hence, it is critical to know both its organic-matter (OM) maturity and its oil/water flow capacity. The introduced Igp considered these features simultaneously; maturity was evaluated by discretizing %Ro from 0 to 1, depending on whether the rock was immature or not; free oil flow capacity modeled the normalizing OSI between 0 and 1 on the basis of results from the Rock-Eval VI pyrolysis (REP) obtained in the laboratory or by electric logs; and water flow capacity was estimated from φFW, obtained using a nuclear-magnetic-resonance (NMR) log, which was transformed into an index between 0 and 1. Flow oil capacity was defined as the amount of moveable oil that exceeded the sorption capacity of the source rock.

Using the Igp is explained with real data from a vertical well that penetrates several stacked shale oil reservoirs. However, the same approach can be used in any other type of wellbore architecture (i.e., deviated, horizontal, geosteered). Initially, a correlation between vertical depth and %Ro was

developed. This resulted in a continuous OM-maturity curve along the well section. Next, OSI was simulated by using a bin porosity from an NMR log, where T2 was between 33 and 80 milliseconds and was correlated with OSI data from REP. As a result, a good match between the simulated and the real OSI data was achieved. Similar to OSI, φFW was also calculated from the NMR log, but it used a bin porosity when T2 was greater than 80 milliseconds. These three parameters were then transformed to fractional indices, which were combined into a unique index, Igp. When the index was greater than 0.66, there was a good chance that the three conditions mentioned above would be met. For the example well considered in this study, it was found that almost 30% of the total vertical section had good moveable oil potential. This corresponded to 10 intervals in the well.

The key novelty of this paper is that we have developed a continuous curve of an index that is easy to use and is powerful for identifying intervals with moveable hydrocarbon potential. This is true even in those intervals without laboratory data because of the continuity of the Igp curve, in addition to the Igp integrated criteria that are usually applied independently. The Igp index is a simple-to-use approach. However, because it is a new method, an explorationist should validate it against real oil production information.


https://doi.org/10.1038/s41598-019-52318-y

Melanosomes (melanin-bearing organelles) are common in the fossil record occurring as dense packs of globular microbodies. The organic component comprising the melanosome, melanin, is often preserved in fossils, allowing identification of the chemical nature of the constituent pigment. In present-day vertebrates, melanosome morphology correlates with their pigment content in selected melanin-containing structures, and this interdependency is employed in the color reconstruction of extinct animals. The lack of analyses integrating the morphology of fossil melanosomes with the chemical identification of pigments, however, makes these inferences tentative. Here, we chemically characterize the melanin content of the soft tissue headcrest of the pterosaur Tupandactylus imperator by alkaline hydrogen peroxide oxidation followed by high-performance liquid chromatography. Our results demonstrate the unequivocal presence of eumelanin in T. imperator headcrest. Scanning electron microscopy followed by statistical analyses, however, reveal that preserved melanosomes containing eumelanin are undistinguishable to pheomelanin-bearing organelles of extant vertebrates. Based on these new findings, straightforward color inferences based on melanosome morphology may not be valid for all fossil vertebrates, and color reconstructions based on ultrastructure alone should be regarded with caution.

Pojjanapornpun, S., Kulsing, C., Kakanopas, P., Nolvachai, Y., Aryusuk, K., Krisnangkura, K., Marriott, P.J., 2019. Simulation of peak position and response profiles in comprehensive two-dimensional gas chromatography. Journal of Chromatography A 1607, 460392.


Approaches to simulate peak time and intensity profiles of compounds in comprehensive two dimensional gas chromatography (GC × GC) were developed, and which are demonstrated for

separation of a mixture of saturated and unsaturated fatty acid methyl esters (FAME) using a range of column sets. The simulation of first and second dimension time (1tR and 2tR) of FAME relies on use of a Gibbs energy additivity approach to correlate with the structures of FAME. First and second dimension peak standard deviations (1σ and 2σ) of the compounds were further calculated from the 1tR and 2tR data according to the plate height concept which provided good agreement between the predicted and experimental peak widths at half height in one dimension GC (1DGC) with an overall R2 of 0.9628. The effect of 1σ distortion caused by the modulation process was also taken into account in the peak width simulation where the simulated 1σ data were rounded up to multiples of the scale of modulation period (PM). Two dimension Gaussian equations were then used to generate GC × GC results (2D contour plots) from simulated 1tR, 2tR, 1σ and 2σ data for FAME separation on different column sets employing ionic liquid and conventional columns. Good overall correlations between experimental and simulated 1tR and 2tR were obtained with R2 of 0.9951 and 0.9802, respectively, and the simulated 2D contour plots were an acceptable match with the experimental results.


https://doi.org/10.1007/s13361-019-02311-6

Various separation and mass spectrometric (MS) techniques have furthered our ability to study complex mixtures, and the desire to measure every analyte in a system is of continual interest. For many complex mixtures, such as the total molecular content of a cell, it is becoming apparent that no one single separation technique or analysis is likely to achieve this goal. Therefore, having a variety of tools to measure the complexity of these mixtures is prudent. Orbitrap MSs are broadly used in systems biology studies due to their unique performance characteristics. However, GC-Orbitraps have only recently become available, and instruments that can use gas chromatography (GC) cannot use liquid chromatography (LC) and vice versa. This limits small molecule analyses, such as those that would be employed for metabolomics, lipidomics, or toxicological studies. Thus, a simple, temporary interface was designed for a GC and Thermo Scientific™ Ion Max housing unit. This interface enables either GC or LC separation to be used on the same MS, an Exactive™ Plus Orbitrap, and utilizes an atmospheric pressure chemical ionization (APCI) source. The GC-APCI interface was tested against a commercially available atmospheric pressure photoionization (APPI) interface for three types of analytes that span the breadth of typical GC analyses: fatty acid methyl esters (FAMEs), polyaromatic hydrocarbons (PAHs), and saturated hydrocarbons. The GC-APCI-Orbitrap had similar or improved performance to the APPI and other reported methods in that it had a lower limit of quantitation, better signal to noise, and lower tendency to fragment analytes.

Prebihalo, S.E., Pinkerton, D.K., Synovec, R.E., 2019. Impact of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry experimental design on data trilinearity and parallel factor analysis deconvolution. Journal of Chromatography A 1605, 460368.


Comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC-TOFMS) is a powerful instrument for the analysis of complex samples.

Deconvolution of overlapped analytes using a suitable chemometric data analysis method such as Parallel Factor Analysis (PARAFAC) is often required. However, PARAFAC is designed to require a strict data trilinearity requirement. In this study we examine how strict this requirement is in the context of GC × GC experimental conditions, and demonstrate that under suitable conditions the data is sufficiently trilinear to achieve accurate deconvolution. The term trilinear deviation ratio (TDR) was previously introduced as a quantitative metric to predict the accuracy of PARAFAC deconvolution. Trilinear deviation ratio is defined as the run-to-run retention time shift, Δ2tR, for a given analyte on the second dimension (2D) separation, divided by the 2D analyte peak width-at-base, 2Wb. We demonstrate that experimental conditions impact the TDR range produced and PARAFAC performance. Column selection and modulation period, PM, are shown to significantly influence the TDR range. Two column sets were evaluated, giving rise to different k’ ranges for the 2D separations. Each column set was used with an optimum PM as well as a longer PM to demonstrate the effect of PM selection on the TDR range and PARAFAC quantification. A PM of 6 s produced a Δ2tR range from −19.5 ms to −98 ms and TDRs from 0.157 to 0.439, translating into a PARAFAC bias from +1.6% to −13.5%. However, a PM of 1.5 s produced a Δ2tR range of −1.1 ms to −8.8 ms, and significantly lower TDRs from 0.013 to 0.057, translating into PARAFAC errors from +2.1% to −3.9%, with an average of −1.1% ± 1.4. These results validate the idea that a suitable GC × GC experimental design will provide accurate quantification with PARAFAC.

Priest, J.A., Hayley, J.L., Smith, W.E., Schultheiss, P., Roberts, J., 2019. PCATS triaxial testing: Geomechanical properties of sediments from pressure cores recovered from the Bay of Bengal during expedition NGHP-02. Marine and Petroleum Geology 108, 424-438.


The Indian National Gas Hydrate Program Expedition 02 (NGHP-02) was the most comprehensive gas hydrate drilling expedition carried out to date. From 74 pressure cores that were successfully recovered from various site locations offshore India, 19 subsamples were obtained for further detailed geotechnical analysis using the PCATS Triaxial apparatus to investigate the geomechanical behaviour of the cores, including small-strain stiffness, Gmax, undrained shear strength, Su, as well as direct-flow measurements of permeability, k. Samples tested included fine-grained muds with no appreciable hydrate through to coarse-grained sands that contained extensive hydrate within the pore space.

Although the subsampling and transfer of pressure cores into the PCATS Triaxial under zero effective confining stress, σ′, remains challenging, 12 samples were successfully transferred and underwent detailed geotechnical characterization. During consolidation, after reapplication of in-situ σ′, all samples experienced axial and radial consolidation, with variations between samples seemingly dependent on the degree of sample disturbance, stress relaxation between coring and testing, hydrate saturation, Sh and grain size, D50. The largest values of Gmax were obtained from samples with high Sh in the pore space, with values much higher than that expected for similar sediments without hydrate under comparable σ’. Samples with high permeability had both high Sh and larger grain size, suggesting that in coarse-grained sediments sufficient pathways are available for reasonable fluid flow even with high hydrate saturations. Triaxial testing and unconfined compression tests highlighted the influence of hydrate on increasing sediment strength, although the size of the sediment grains appeared to have an important control on the magnitude of the strength increase and the overall stress-strain behaviour.

The results from the detailed geotechnical characterization of the recovered pressure cores will be invaluable in helping India identify potential locations for future gas production wells, and assess the long-term performance of such reservoirs.

Psillakis, E., Koutela, N., Colussi, A.J., 2019. Vacuum-assisted headspace single-drop microextraction: Eliminating interfacial gas-phase limitations. Analytica Chimica Acta 1092, 9-16.


Gas-phase limitations have been neglected in headspace single-drop microextraction (HS-SDME) and rate control has been assumed to primarily reside in the liquid water and/or organic phases, but not in the headspace. Herein we demonstrate the presence of interfacial gas constraints and propose using reduced headspace pressures to remove them. To describe the pressure dependence of HS-SDME, the system was decoupled into two interfacial steps: (i) the evaporation step (water-headspace interface) formulated using the two-film theory and (ii) the analyte uptake by the microdrop (headspace-microdrop interface) formulated using the resistance model. Naphthalene, acenaphthene, and pyrene were chosen as model analytes for their large Henry’s law solubility constants in n-octanol (HOA > 103 M atm−1), and their low to moderate Henry’s law volatility constants in water as a solvent (KH). We have found that extraction times were significantly shortened for all analytes by sampling at pressures well below the 1 atm used in the standard HS-SDME procedure. The acceleration of naphthalene extraction, whose facile evaporation into the headspace had been assumed to be practically pressure independent, highlighted the role of mass transfer through the interfacial gas layer on the organic solvent drop. The larger accelerations observed for acenaphthene and (especially) pyrene upon reducing the sampling pressure, suggested that gas-sided constraints were important during both the evaporation and uptake steps. Model calculations incorporating mass transfers at the headspace-microdrop interface confirmed that gas-phase resistance is largely eliminated (>96%) when reducing the sampling pressure from 1 to 0.04 atm, an effect that is nearly independent of analyte molecular mass. The relative importance of the two interfacial steps and their gas- and liquid-phase limitations are discussed, next to the use of KH and HOA to predict the positive effect of vacuum on HS-SDME.



Cyclothems, composed of interbedded mudstone, coal and sandstone layers, make up the Taiyuan and Shanxi Formations in the Late Carboniferous to Early Permian in North China under a marine-to-continental depositional environment. The cyclothems act as important fossil energy hosts, such as coalbeds, hydrocarbon source rocks and unconventional natural gas reservoirs. Organic geochemistry and petrology of mudstones and coals in the Taiyuan and Shanxi Formations in the eastern Ordos Basin were studied to reveal the organic matter sources and paleoenvironments. Total organic carbon (TOC) contents vary from 1.1 wt% (mudstone) to 72.6 wt% (coal). The samples are mainly within the oil window, with the Tmax values ranging from 433 to 469 °C. Organic petrology and source biomarkers indicate that the mudstones were sourced from a mixed organic matter

input, and terrigenous organic matter predominates over aquatic organic matter. The coals are mostly sourced by terrigenous organic matter inputs. High concentrations of hopanes argue for a strong bacterial input. Some m/z 217 mass chromatograms have peaks at the hopanes' retention times as a result of high hopane to sterane ratios. These hopane-derived peaks do not interfere the identification of the steranes because the hopanes and the steranes have different retention times. Maturity-dependent biomarkers demonstrate that the samples have been thermally mature, which agree with the Tmax values. Anomalously low C29 20S/(20S + 20R) and C29 ββ/(ββ + αα) sterane ratios are present in all the samples, and are interpreted as due to the terrigenous organic matter input or the coal-related depositional environment. In addition, biomarkers and iron sulfide morphology indicate that the organic matter of the mudstones deposited in a proximal setting with shallow, brackish/fresh water bodies. With consideration of preservation of organic matter, the redox conditions are dysoxic. Redox oscillations resulted in the records of oxic conditions in some samples. Finally, the coals and the mudstones mainly generate gas and have poor oil generative potential.



The coal measure gas (CMG) development in Surat Basin, Australia has achieved great success, thus providing new inspiration for solving dilemmas faced by the coalbed methane (CBM) industry in China. The success depends on the reservoir-forming geological conditions derived from the frequent interbedding of thin coal seams and clastic rocks, and two essential aspects are as below:firstly, the single gas-bearing reservoir in this coal measures are relatively thin, but its accumulated hydrocarbon generation potential is huge, and thus can be developed into a high-quality composite gas reservoir; secondly, the thin interbedded reservoir is more conducive to the development of natural fractures, laying a key foundation for the development of high-permeability composite reservoir. In addition, the many and thin coal measures have a large contact surface with the surrounding rocks while ensuring the gas generating capacity, which is conducive to the transformation of CBM into coal measure free gas and also helpful to coal dehydration and the desorption and production of CBM. Coal-bearing strata that have the basic geological conditions similar to the coal-bearing system in Surat Basin are not uncommon in China, such as the Lower Cretaceous in the eastern Inner Mongolia, the Upper Carboniferous in the western margin of Ordos Basin, the Upper Triassic in the western Sichuan Basin, and the Upper Triassic in Chuxiong Basin. It is suggested to pay attention to the new fields and new layers of this type of CMG, and based on the specific parameters and ideas, carry out special evaluation research and special exploration for these areas and coal measures, laying a new natural gas resource foundation to guarantee the national oil and gas security strategy of "increasing reserves and production".

Quist, A.J.L., Rohlman, D.S., Kwok, R.K., Stewart, P.A., Stenzel, M.R., Blair, A., Miller, A.K., Curry, M.D., Sandler, D.P., Engel, L.S., 2019. Deepwater Horizon oil spill exposures and neurobehavioral function in Gulf study participants. Environmental Research 179, 108834.


Introduction: The 2010 Deepwater Horizon (DWH) disaster exposed tens of thousands of oil spill response and cleanup (OSRC) workers to hydrocarbons and other hazardous chemicals. Some

hydrocarbons, such as toluene and hexane, have been found to have acute adverse effects on the central nervous system in occupational settings. However, no studies have examined the association between oil spill exposures and neurobehavioral function.

Methods: We used data from the Gulf Long-term Follow-up Study, a cohort of adults who worked on the DWH response and cleanup. Total hydrocarbon (THC) exposure attributed to oil spill cleanup work was estimated from a job-exposure matrix linking air measurement data to detailed cleanup work histories. Participants were also categorized into 6 job categories, or OSRC classes, based on their activity with the highest exposure. Neurobehavioral performance was assessed at a clinical exam 4–6 years after the spill. We used multivariable linear regression to evaluate relationships of ordinal THC levels and OSRC classes with 16 neurobehavioral outcomes.

Results: We found limited evidence of associations between THC levels or OSRC classes and decreased neurobehavioral function, including attention, memory, and executive function. Workers exposed to ≥3 ppm THC scored significantly worse (difference1.0–2.9ppm = -0.39, 95% confidence interval (CI) = -0.74, −0.04) than workers exposed to <0.30 ppm THC for the digit span forward count test. There was also a possible threshold effect above 1 ppm THC for symbol digit test total errors (difference1.0–2.9ppm = −0.56 (95% CI = −1.13, −0.003), difference≥3.0ppm = −0.55 (95% CI = −1.20, 0.10)). Associations appeared to be stronger in men than in women. A summary latency measure suggested an association between more highly exposed jobs (especially support of operations workers) and decreased neurobehavioral function.

Conclusion: OSRC-related exposures were associated with modest decreases in neurobehavioral function, especially attention, memory, and executive function.

Rapin, W., Ehlmann, B.L., Dromart, G., Schieber, J., Thomas, N.H., Fischer, W.W., Fox, V.K., Stein, N.T., Nachon, M., Clark, B.C., Kah, L.C., Thompson, L., Meyer, H.A., Gabriel, T.S.J., Hardgrove, C., Mangold, N., Rivera-Hernandez, F., Wiens, R.C., Vasavada, A.R., 2019. An interval of high salinity in ancient Gale crater lake on Mars. Nature Geoscience 12, 889-895.

https://doi.org/10.1038/s41561-019-0458-8

Precipitated minerals, including salts, are primary tracers of atmospheric conditions and water chemistry in lake basins. Ongoing in situ exploration by the Curiosity rover of Hesperian (around 3.3–3.7 Gyr old) sedimentary rocks within Gale crater on Mars has revealed clay-bearing fluvio-lacustrine deposits with sporadic occurrences of sulfate minerals, primarily as late-stage diagenetic veins and concretions. Here we report bulk enrichments, disseminated in the bedrock, of 30–50 wt% calcium sulfate intermittently over about 150 m of stratigraphy, and of 26–36 wt% hydrated magnesium sulfate within a thinner section of strata. We use geochemical analysis, primarily from the ChemCam laser-induced breakdown spectrometer, combined with results from other rover instruments, to characterize the enrichments and their lithology. The deposits are consistent with early diagenetic, pre-compaction salt precipitation from brines concentrated by evaporation, including magnesium sulfate-rich brines from extreme evaporative concentration. This saline interval represents a substantial hydrological perturbation of the lake basin, which may reflect variations in Mars’ obliquity and orbital parameters. Our findings support stepwise changes in Martian climate during the Hesperian, leading to more arid and sulfate-dominated environments as previously inferred from orbital observations.

Rastelli, E., Corinaldesi, C., Dell’Anno, A., Tangherlini, M., Lo Martire, M., Nishizawa, M., Nomaki, H., Nunoura, T., Danovaro, R., 2019. Drivers of bacterial α- and β-diversity patterns and functioning in subsurface hadal sediments. Frontiers in Microbiology 10, 2609. doi: 10.3389/fmicb.2019.02609.


Oceanic trenches at hadal (>6,000 m) depths are hot spots of organic matter deposition and mineralization and can host abundant and active bacterial assemblages. However, the factors able to shape their biodiversity and functioning remain largely unexplored, especially in subsurface sediments. Here, we investigated the patterns and drivers of benthic bacterial α- and β-diversity (i.e., OTU richness and turnover diversity) along the vertical profile down to 1.5 m sediment depth in the Izu-Bonin Trench (at ~10,000 m water depth). The protease and glucosidase enzymatic activity rates were also determined, as a proxy of organic matter degradation potential in the different sediment layers. Molecular fingerprinting based on automated ribosomal intergenic spacer analysis (ARISA) indicated that the α-diversity of bacterial assemblages remained high throughout the vertical profile and that the turnover (β-) diversity among sediment horizons reached values up to 90% of dissimilarity. Multivariate distance-based linear modeling (DISTLM) pointed out that the diversity and functioning of the hadal bacterial assemblages were influenced by the variability of environmental conditions (including the availability of organic resources and electron donors/acceptors) and of viral production rates along the sediment vertical profile. Based on our results, we can argue that the heterogeneity of physical-chemical features of the hadal sediments of the Izu-Bonin Trench contribute to increase the niches availability for different bacterial taxa, while viruses contribute to maintain high levels of bacterial turnover diversity and to enhance organic matter cycling in these extremely remote and isolated ecosystems.

Rathinam, N.K., Gorky, Bibra, M., Salem, D.R., Sani, R.K., 2020. Bioelectrochemical approach for enhancing lignocellulose degradation and biofilm formation in Geobacillus strain WSUCF1. Bioresource Technology 295, 122271.


Investigations on microbial electrocatalysis as a strategy for enhancing the rates of substrate utilization leading to enhanced yield of biomass and enhanced biofilm formation are reported. A thermophilic Geobacillus sp. strain WSUCF1 (60 °C), a potential lignocellulose degrading microorganism was used as the electrocatalyst. Glucose, cellulose, and corn stover were used as the feedstocks. The results of this investigation showed that applying the oxidation potential of −0.383 mV (vs PRE) increased the glucose utilization and COD removal by 25.5% and 29.7% respectively. The bioelectrocatalysis strategy also increased the biomass yield by 81.2, 42.1, and 49.5% in the case of systems fed with glucose, cellulose, and corn stover, respectively, when compared with the systems without applied oxidation potential. This is the first work reporting the effects of applied oxidation potential on increasing the rates of degradation of lignocellulosic biomass and enhanced biofilm formation.

Rathnaweera, T.D., Ranjith, P.G., 2020. Nano-modified CO2 for enhanced deep saline CO2 sequestration: A review and perspective study. Earth-Science Reviews 200, 103035.


CO2 sequestration in deep saline aquifers has been well-established as a mode of reducing the anthropogenic emissions of CO2 and mitigating the risks associated with human-induced global warming. The long-term success of a deep saline sequestration project depends in particular on the volume of CO2 sequestrated and the prevention of risk of leakage. However, current practice still suffers from the slow solubility of injected CO2 in brine, making conventional versions of the process inefficient, uneconomical, and unsafe. Therefore, the aim of this study is to review current techniques and propose a new high-performance technique for CO2 sequestration in deep saline aquifers, by introducing nanoparticles into injected CO2. Nanoparticles are considered promising tools for improved seepage efficacy in the petroleum industry, and studies of CO2 sequestration have led to exciting developments in the last few years. Unfortunately, our knowledge of the complex interaction between nanoparticles, CO2 and reservoir pore fluid and its feedback on other operational and reservoir parameters are poorly understood. The first part of this article gives an overview of conventional mixing of CO2 and how nano-injection improves convective mixing, based on critical wavelengths and critical onset times calculated using thirty-two saline aquifers around the world. In addition, several different nano-injection methods and possible nanomaterials for deep saline sequestration are discussed. The second part of this article considers the influence of nano-injection on gravity, viscous and capillary forces and how these non-linear alterations change the conventional mechanism of CO2 plume development, and the propagation and transport characteristics of CO2 in porous media based on the wettability, interfacial tension and solubility modifications which occur with the introduction of nanoparticles into the CO2 stream. The proposed technique promises to enhance CO2 storage capacity, reduce operational and monitoring costs, and minimize the risk of leakage to nearby freshwater aquifers. This study generates valuable new science, applied in technology that can be used for real-world CO2 storage enhancement in pilot and field-scale projects. However, further research in related areas is required.



CO2 cyclic stimulation (huff and puff) is a method for increasing well productivity after primary and secondary production. In this work, we study the feasibility and estimated enhanced oil recovery of CO2 huff and puff for light oil low-pressure and low-permeability reservoirs using numerical simulation supported by experimental and field test data. We performed CO2 huff and puff numerical modeling to (1) understand the effect of operational and geological parameters on incremental oil recovery and (2) also history match a huff and puff pilot test. The reservoir model is based on available geologic data and experimental PVT data in depleted oil reservoirs similar to those in the Appalachian Basin. The previous huff and puff operations in the Appalachian basin have been used in a wide range of operational parameters such as CO2 injected mass and CO2 cycles. Simulation results in this study, using a pseudomiscible approach in a black oil model, show that the injection rate and the mixing parameter are the main parameters affecting incremental oil recovery. There is a nonlinear relationship between CO2 injected mass (beyond 200 MT) and incremental recovery. Also, permeability heterogeneity can significantly affect CO2 huff and puff performance and should be accounted in the model. In addition to the parametric study, numerical simulations focusing on matching primary production data and pressure data from the CO2 injection period during a huff and puff pilot test in a depleted oil reservoir were performed with sensitivity to

uncertain parameters. Homogenous and composite single wellbore models were built for the history match. Uncertain parameters include the permeability of each zone and relative permeability relationships. Simulation results of the matched model show the importance of considering bottom hole pressure during huff and puff as a matching parameter to evaluate the model’s uncertain parameters (such as permeability) accurately. A comparison of the oil–water relative permeability of the matched model with the core-flood experimental data, using a Clinton sandstone core, is also discussed.

Reda, R., Saffaj, T., Ilham, B., Saidi, O., Issam, K., Brahim, L., El Hadrami, E.M., 2019. A comparative study between a new method and other machine learning algorithms for soil organic carbon and total nitrogen prediction using near infrared spectroscopy. Chemometrics and Intelligent Laboratory Systems 195, 103873.


Soil organic carbon (SOC) and total nitrogen (TN) are essential elements in agricultural soil and play an important role in many biological and chemical activities for plant growth. The assessment of these parameters in the soil is crucial in agriculture. The problem with traditional chemical analysis methods for SOC and TN is that they are time and resource consuming. In recent years, near-infrared (NIR) spectroscopy has been used as an alternative for SOC and TN determination. Accordingly, in this study, a new approach based on the ensemble learning modelling (ELM) algorithm is used to predict SOC and TN. This approach uses six partial least squares regression (PLS) models with six pre-processing methods as learners for this method. The output of this approach is computed by averaging the predicted values computed by its constituent learners. This algorithm is used to predict the amount of SOC and TN of Moroccan soil collected from four agricultural regions using NIR. The performance of this algorithm is compared with separated regression models, namely PLS, back-propagation neural network (BPNN) with and without variable selection (VS) algorithms. using three metrics, R2, root mean square error (RMSE), and the ratio of performance to deviation (RPD) calculated by a validation dataset. The results show that the ELM outperformed all PLS models and BPNN with and without VS for both elements. Furthermore, BPNN without VS and PLS provided better performance than PBNN with VS for SOC prediction. However, for TN, PLS gave a moderate performance according to other models (R2 = 0.80 and RPD = 2.77). The best predictions were obtained with the E-L model for SOC (R2 = 0.96, RMSE = 1.92, and RPD = 4.87) and TN (R2 = 0.94, RMSE = 0.57, and RPD = 4.91), which classified the model as an excellent one for SOC and TN prediction. The proposed method ELM has the advantage of wider applicability and better performance for TN and SOC quantification by NIR spectroscopy in comparison with separated PLS and BPNN with and without VS.

Reusser, J.E., Verel, R., Zindel, D., Frossard, E., McLaren, T.I., 2019. Identification of lower-order inositol phosphates (IP5 and IP4) in soil extracts as determined by hypobromite oxidation and solution 31P NMR spectroscopy. Biogeosciences Discussions 2019, 1-28.


Inositol phosphates (IP) are a major pool of identifiable organic phosphorus (P) in soil. However, insight on their distribution and cycling in soil remains limited, particularly of lower-order IP (IP5 and IP4). This is because their quantification typically requires a series of chemical extractions, including

hypobromite oxidation to isolate IP, followed by chromatographic separation. Here, for the first time, we identify the chemical nature of organic P in four soil extracts following hypobromite oxidation using solution 31P NMR spectroscopy and transverse relaxation (T2) experiments. Soil samples analysed include the A horizon of a Ferralsol from Colombia, of a Cambisol from Switzerland, of a Gleysol from Switzerland and of a Cambisol from Germany. Solution 31P NMR spectra of the phosphomonoester region on soil extracts following hypobromite oxidation revealed an increase in the number of sharp signals (up to 70), and an on average 2-fold decrease in the concentration of the broad signal compared to the untreated soil extracts. We identified the presence of four stereoisomers of IP6, four stereoisomers of IP5, and scyllo-IP4 (using solution 31P NMR spectroscopy). We also identified for the first time two isomers of myo-IP5 in soil extracts: myo-(1,2,4,5,6)-IP5 and myo-(1,3,4,5,6)-IP5. Concentrations of total IP ranged from 1.4 to 159.3 mg P/kgsoil across all soils, of which between 9 % and 50 % were comprised of lower-order IP. Furthermore, we found that the T2 times, which are considered to be inversely related to the tumbling of a molecule in solution and hence its molecular size, were significantly shorter for the underlying broad signal compared to the sharp signals (IP6) in soil extracts following hypobromite oxidation. In summary, we demonstrate the presence of a plethora of organic P compounds in soil extracts, largely attributed to IP of various order, and provide new insight on the chemical stability of complex forms of organic P associated with soil organic matter.

Řezanka, T., Vítová, M., Lukavský, J., Nedbalová, L., Kolouchová, I., 2019. Rapid screening of very long-chain fatty acids from microorganisms. Journal of Chromatography A 1605, 460365.


The analysis of triacylglycerols and phospholipids - phosphatidylcholines allowed the use of shotgun lipidomics to identify very long-chain fatty acids and very long-chain polyunsaturated fatty acids in microalgae. These fatty acids were determined in triacylglycerols by positive electrospray ionization of neutral loss scans of different fatty acids, e.g. 24:0, 24:1ω9, 24:6ω3, 26:0, 26:1ω9, 28:0, 28:1ω9, 28:2ω6, and 28:8ω3. Likewise, very long-chain fatty acids in phosphatidylcholines were identified by negative electrospray ionization mass spectrometry in the selected ion-monitoring of the two most important ions (R1COO− and R2COO−). The limit of detection was determined at 10 nmol/L (∼11 pg/μL) in triacylglycerols and 8.6 nmoles/L (∼8 pg/μL) in phosphatidylcholines. The use of liquid chromatography–mass spectrometry is suitable for very long-chain polyunsaturated fatty acids with up to 8 double bonds due to the time of analysis as well as for reasons of lower thermal stability of polyunsaturated fatty acids towards saturated fatty acids, but gas chromatography–mass spectrometry is better suited for the analysis of saturated very long-chain fatty acids.

Ringrose, P.S., Meckel, T.A., 2019. Maturing global CO2 storage resources on offshore continental margins to achieve 2DS emissions reductions. Scientific Reports 9, 17944.

https://doi.org/10.1038/s41598-019-54363-z

Most studies on CO2 emissions reduction strategies that address the ‘two-degree scenario’ (2DS) recognize a significant role for CCS. For CCS to be effective, it must be deployed globally on both existing and emerging energy systems. For nations with large-scale emissions, offshore geologic CO2 storage provides an attractive and efficient long-term strategy. While some nations are already developing CCS projects using offshore CO2 storage resources, most geographic regions have yet to

begin. This paper demonstrates the geologic significance of global continental margins for providing broadly-equitable, geographically-relevant, and high-quality CO2 storage resources. We then use principles of pore-space utilization and subsurface pressure constraints together with analogs of historic industry well deployment rates to demonstrate how the required storage capacity can be developed as a function of time and technical maturity to enable the global deployment of offshore storage for facilitating 2DS. Our analysis indicates that 10–14 thousand CO2 injection wells will be needed globally by 2050 to achieve this goal.

Roberts, J., Heij, G., Elmore, R.D., 2019. Palaeomagnetic dating of hydrothermal alteration in the Woodford Shale, Oklahoma, USA. Geological Magazine 156, 2043-2052.

https://doi.org/10.1017/S0016756819000360

An oriented Woodford Shale core from the eastern Ardmore Basin was sampled to test if the shale was an open or closed system to hydrothermal fluids, and to determine the timing of alteration. Mineralized fractures are ubiquitous in the core, and the shale exhibits a complex paragenesis with multiple hydrothermal minerals, including biotite, magnesite, norsethite, gorceixite and potassium feldspar present in and around the fractures. These minerals suggest that the Woodford Shale was an open system during part of its diagenetic history. Vitrinite reflectance (Ro) measurements indicate values of ∼1.81 % (∼230 °C). Palaeomagnetic analysis reveals a characteristic remanent magnetization (ChRM) with south-southeasterly declinations and shallow inclinations that resides in magnetite. This ChRM is interpreted to be either a chemical remanent magnetization (CRM) or a thermochemical remanent magnetization (TCRM) that was acquired at 245 ± 10 Ma during Late Permian time based on the pole position (51.0° N, 115.6° E). Because the palaeomagnetic specimens show evidence of extensive hydrothermal alteration, the CRM/TCRM is interpreted to date the migration of hydrothermal fluids through the shale. The agreement in timing with other studies that report hydrothermal alteration in southern Oklahoma and the Ouachita Mountains in Late Permian time, suggest that there were post-collisional fluid-flow events which accessed reservoirs of warm fluids.

Rodríguez-Hidalgo, A., Morales, J.I., Cebrià, A., Courtenay, L.A., Fernández-Marchena, J.L., García-Argudo, G., Marín, J., Saladié, P., Soto, M., Tejero, J.M., Fullola, J.M., 2019. The Châtelperronian Neanderthals of Cova Foradada (Calafell, Spain) used imperial eagle phalanges for symbolic purposes. Science Advances 5, eaax1984.

http://advances.sciencemag.org/content/5/11/eaax1984.abstract

Evidence for the symbolic behavior of Neanderthals in the use of personal ornaments is relatively scarce. Among the few ornaments documented, eagle talons, which were presumably used as pendants, are the most frequently recorded. This phenomenon appears concentrated in a specific area of southern Europe during a span of 80 thousand years. Here, we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this symbolic behavior, providing the first documentation of its use among the Iberian populations, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Middle Paleolithic time frame, including their presence among the last Neanderthal populations, raises the question of the

survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages and beyond.

Rodríguez-Sánchez, S., Soria, A.C., Lebrón-Aguilar, R., Sanz, M.L., Ruiz-Matute, A.I., 2019. Evaluation of different ionic liquid stationary phases for the analysis of carbohydrates by gas chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry 411, 7461-7472.

https://doi.org/10.1007/s00216-019-02118-0

Five commercial ionic liquid (IL) columns have been evaluated for the first time for the gas chromatography-mass spectrometry (GC-MS) analysis of low molecular weight carbohydrate (LMWC) standards (mono-, di-, and trisaccharides, inositols, and iminosugars). A previous derivatization step was necessary to convert the LMWCs into their volatile and stable derivatives. Compared with conventional GC stationary phases, such as HP-1 and Supelcowax® 10, IL columns have shown a different selectivity in the separation of target compounds. Among the IL columns, only SLB™-IL82 allowed the elution of all the LMWCs studied. Its performance in terms of peak width and asymmetry, evaluated under different oven temperature conditions, was shown to be dependent on the carbohydrate class considered. As an example of application, a SLB™-IL82 column was successfully used to separate the complex mixtures of LMWCs in hyacinth and mulberry extracts. This column is an interesting alternative to the conventional stationary phases used in the GC analysis of LMWCs in real-world samples.

Roelofse, C., Alves, T.M., Gafeira, J., 2020. Structural controls on shallow fluid flow and associated pockmark fields in the East Breaks area, northern Gulf of Mexico. Marine and Petroleum Geology 112, 104074.


Three-dimensional (3D) seismic data, combined with semi-automated mapping in ArcGIS, were used to analyse the morphology and distribution of 720 pockmarks and 62 mud volcanoes in the northern Gulf of Mexico. The relationship amongst salt bodies, faults and the distribution of pockmarks and mud volcanoes stresses the significance of these structures in focusing fluid flow on continental margins. The pockmarks were classified according to their structural setting and depth of source, and later correlated with seep data from the Bureau of Ocean Energy Management (BOEM). Key findings include: a) half of the pockmarks are located within faults rooted on the top of salt diapirs, whilst 96% of the pockmarks are associated with salt diapirs – emphasising the importance of salt and crestal faults in focusing fluid flow to the sea floor; b) diffusion flow through the salt minibasins is clear due to the presence of soft amplitude anomalies (indicating fluids) and pockmarks located far from salt or faults; c) oil and gas are actively leaking to the sea floor; d) a higher density of fluid flow features are found in areas with steeper minibasin dips and greater catchment areas. While no clear correlation is evident between the morphological attributes and depth of source, the shallow plumbing system is dominated by pockmarks, whereas mud volcanoes are sourced from the deeper parts of the salt minibasins. In summary, this study uses a novel approach to analyse the plumbing system in a salt-rich basin based on the recognition of surface fluid flow features. The importance of characterising the fluid flow features and associated structures to reduce risk and uncertainty is stressed in terms of both shallow gas hazards and hydrocarbon leakage from deeper reservoirs.

Rohal, M., Barrera, N., Van Eenennaam, J.S., Foekema, E.M., Montagna, P.A., Murk, A.J., Pryor, M., Romero, I.C., 2020. The effects of experimental oil-contaminated marine snow on meiofauna in a microcosm. Marine Pollution Bulletin 150, 110656.


During an oil spill, a marine oil snow sedimentation and flocculent accumulation (MOSSFA) event can transport oil residue to the seafloor. Microcosm experiments were used to test the effects of oil residues on meiofaunal abundance and the nematode:copepod ratio under different oil concentrations and in the presence and absence of marine snow. Total meiofaunal abundance was 1.7 times higher in the presence of snow regardless of oil concentration. The nematode:copepod ratio was 13.9 times lower in the snow treatment regardless of the oil concentration. Copepod abundance was 24.3 times higher in marine snow treatments and 4.3 times higher at the highest oil concentration. Nematode abundance was 1.7 times lower at the highest oil concentration. The result of the experiment was an enrichment effect. The lack of a toxic response in the experiments may be attributable to relatively low oil concentrations, weathering processes, and the absence of chemically dispersed oil.

Römer, M., Hsu, C.-W., Loher, M., MacDonald, I.R., dos Santos Ferreira, C., Pape, T., Mau, S., Bohrmann, G., Sahling, H., 2019. Amount and fate of gas and oil discharged at 3400 m water depth from a natural seep site in the southern Gulf of Mexico. Frontiers in Marine Science 6, 700. doi: 10.3389/fmars.2019.00700.


This multi-disciplinary study of the hydrocarbon seepage system at Tsanyao Yang Knoll (TYK) in the southern Gulf of Mexico illustrates the amount and fate of hydrocarbons (mainly oil and methane) emanating from the seafloor structure and rising through a 3400 m water column. TYK forms part of the Campeche Knolls and was found to be one of the most active seepage structures at such an exceptional depth. Combining ship-based and AUV-based hydroacoustic mapping with direct seafloor observations and investigations, which used a TV-sled and a remotely operated vehicle with gas and water sampling devices provided an integrated view for the various transport pathways of hydrocarbons from the seafloor to the sea surface. In total, 32 acoustic ‘flares,’ indicative of gas bubble emission sites, were detected emanating from depressions on top of the knoll. Most of the emission sites were concentrated in two depressions that comprised a main seep field. An estimated volume of 550–4650 L of hydrocarbons per hour (or 8300–70,600 mol CH<sub>4</sub> per hour) are released in the form of gas bubbles, which dissolve almost entirely during their rise in the water column. However, echograms showed gas anomalies to about 500 m below sea surface and some bubbles were seen to burst at the sea surface. Concentrations of dissolved methane were highly elevated (∼30,000 nmol/L) directly above the seafloor emission site, but decreased to background concentrations (3–5 nmol/L) within the lowermost 100 m. Smaller volume flow rates of oil also escaped from the seafloor, rose to the sea surface and generated natural oil slicks visible from the ship and in satellite images. This study shows that hydrocarbon seepage at ∼3400 m water depth can be followed to the sea surface. However, most of the methane dissolves in deeper waters, whereas oil reaches the sea surface.



Abstract: Magnetosomes are membrane-enveloped single-domain ferromagnetic nanoparticles enabling the navigation of magnetotactic bacteria along magnetic field lines. Strict control over each step of biomineralization generates particles of high crystallinity, strong magnetization, and remarkable uniformity in size and shape, which is particularly interesting for many biomedical and biotechnological applications. However, to understand the physicochemical processes involved in magnetite biomineralization, close and precise monitoring of particle production is required. Commonly used techniques, such as transmission electron microscopy (TEM) or Fe measurements, allow only for semiquantitative assessment of the magnetosome formation without routinely revealing quantitative structural information. In this study, lab-based small-angle X-ray scattering (SAXS) is explored as a means to monitor the different stages of magnetosome biogenesis in the model organism Magnetospirillum gryphiswaldense. SAXS is evaluated as a quantitative stand-alone technique to analyze the size, shape, and arrangement of magnetosomes in cells cultivated under different growth conditions. By applying a simple and robust fitting procedure based on spheres aligned in linear chains, it is demonstrated that the SAXS data sets contain information on both the diameter of the inorganic crystal and the protein-rich magnetosome membrane. The analyses corroborate a narrow particle size distribution with an overall magnetosome radius of 19 nm in Magnetospirillum gryphiswaldense. Furthermore, the averaged distance between individual magnetosomes is determined, revealing a chain-like particle arrangement with a center-to-center distance of 53 nm. Overall, these data demonstrate that SAXS can be used as a novel stand-alone technique allowing for the at-line monitoring of magnetosome biosynthesis, thereby providing accurate information on the particle nanostructure.

Importance: This study explores lab-based small-angle X-ray scattering (SAXS) as a novel quantitative stand-alone technique to monitor the size, shape, and arrangement of magnetosomes during different stages of particle biogenesis in the model organism Magnetospirillum gryphiswaldense. The SAXS data sets contain volume-averaged, statistically accurate information on both the diameter of the inorganic nanocrystal and the enveloping protein-rich magnetosome membrane. As a robust and nondestructive in situ technique, SAXS can provide new insights into the physicochemical steps involved in the biosynthesis of magnetosome nanoparticles as well as their assembly into well-ordered chains. The proposed fit model can easily be adapted to account for different particle shapes and arrangements produced by other strains of magnetotactic bacteria, thus rendering SAXS a highly versatile method.

Roy, D., Wahab, M.F., Berger, T.A., Armstrong, D.W., 2019. Ramifications and insights on the role of water in chiral sub/supercritical fluid chromatography. Analytical Chemistry 91, 14672-14680.


More than 40 cosolvents have been used with carbon dioxide to alter its solvation strength. Among the most interesting systems is the subcritical/supercritical CO2/alkanol eluents. Using small amounts of water in CO2/MeOH is known to be beneficial in chiral subcritical/supercritical chromatography. However, the ramifications of introducing water as a cosolvent component is not

entirely understood. In this work, we demonstrate important aspects of the CO2/MeOH/H2O system on nine chiral stationary phases with very different surface chemistries, encompassing derivatized polysaccharides, macrocyclic glycopeptides, iso-butylmercaptoquinine, isopropyl macrocyclic oligosaccharides, and π-electron acceptor/π-electron donor phases. A hydrophilicity scale has been shown to be useful in predicting if a given chiral column chemistry would show a significant enhancement in separation efficiency in the presence of water in the CO2/MeOH system. We demonstrate up to 8-fold enhancements in plate counts of chiral separations with a concomitant decrease in retention times, as predicted by the qualitative test. The same chiral analysis can now be completed in almost a third of the time with the addition of small amounts of water, thereby decreasing organic solvent consumption by a considerable amount. Hydrophobic stationary phases show a minimal increase in efficiency and decrease in analysis times and optimized separations show much larger reduced plate heights, compared to more hydrophilic stationary phases. Furthermore, the presence of water can alter the nature of the adsorption isotherm under nonlinear conditions. Small amounts of water can be used to tune nonlinear tailing peaks into fronting ones, significantly improving preparative enantiomeric separations.

Ruginescu, R., Purcărea, C., Dorador, C., Lavin, P., Cojoc, R., Neagu, S., Lucaci, I., Enache, M., 2019. Exploring the hydrolytic potential of cultured halophilic bacteria isolated from the Atacama Desert. FEMS Microbiology Letters 366.


Considering that most industrial processes are carried out under harsh physicochemical conditions, which would inactivate enzymes from commonly isolated mesophilic organisms, current studies are geared toward the identification of extremophilic microorganisms producing enzymes resistant to extreme salt concentrations, temperature and pH. Among the extremophiles, halophilic microorganisms are an important source of salt-tolerant enzymes that can be used in varying biotechnological applications. In this context, the aim of the present work was to isolate and identify halophiles producing hydrolases from the Atacama Desert, one of the harshest environments on Earth. Isolates were recovered from halite samples and screened for the presence of seven different hydrolase activities (amylase, caseinase, gelatinase, lipase, pectinase, cellulase and inulinase) using agar plate-based assays. From a total of 23 halophilic bacterial isolates, most showed lipolytic (19 strains) and pectinolytic (11 strains) activities. The molecular identification of eight selected isolates showed a strong similarity to members of the Halomonas and Idiomarina genera. Therefore, the present study represents a preliminary, but essential, step to identify novel biological sources of extremozymes in an environment once thought to be devoid of life.


https://doi.org/10.1038/s41467-019-13156-8

Seismic velocity measurements have revealed that the Tohoku-Oki earthquake affected velocity structures of volcanic zones far from the epicenter. Using a seismological method based on ambient seismic noise interferometry, we monitored the anisotropy in the Mount Fuji area during the year 2011, in which the Tohoku-Oki earthquake occurred (Mw = 9.0). Here we show that even at 400 km

from the epicenter, temporal variations of seismic anisotropy were observed. These variations can be explained by changes in the alignment of cracks or fluid inclusions beneath the volcanic area due to stress perturbations and the propagation of a hydrothermal fluid surge beneath the Hakone hydrothermal volcanic area. Our results demonstrate how a better understanding of the origin of anisotropy and its temporal changes beneath volcanoes and in the crust can provide insight into active processes, and can be used as part of a suite of volcanic monitoring and forecasting tools.

Sadooni, F.N., Alsharhan, A.S., 2019. Regional stratigraphy, facies distribution, and hydrocarbons potential of the Oligocene strata across the Arabian Plate and Western Iran. Carbonates and Evaporites 34, 1757-1770.

https://doi.org/10.1007/s13146-019-00521-3

Major global events during the Oligocene epoch included a climatic change from warm “greenhouse” to a cooler “icehouse” that was accompanied by the onset of Antarctic glaciation. These events led to decline in water temperature, salinity, nutrient supply and oxygen levels, and the extinction of some major fauna and flora. Within the study area, during this epoch, the shrinkage of the Neotethys and the development of the Paratethys, the collision of Arabia with Eurasia and the development of the Zagros mountains and opening of the Red Sea which led eventually to the separation of Arabia from Africa were witnessed. Oligocene sediments are absent from most parts of the Arabian Plate but are well-preserved in western and southwestern Iran. The most well-developed strata are the coral reefs of the Kirkuk Group in northern Iraq and the shallow water carbonates of the Asmari Formation in southwestern Iran. The study area also represents the birthplace of commercial hydrocarbons production in the Middle East from these sediments in Masjid-i-Sulaiman Field in Iran and Kirkuk Field in Iraq at the first decade of the last century. Future exploration for hydrocarbons potential should focus on identifying subsurface coral buildups or clastic strata that are equivalent to the Asmari Formation in Iran.

Saito, S., Hsiung, K.-H., Sanada, Y., Moe, K., Hamada, Y., Nakamura, Y., Wu, H.-Y., Shinmoto, Y., Yamada, Y., 2019. Gas hydrate occurrence and distribution controlled by regional geological structure off eastern India: Estimates from logging-while-drilling in Area-B, National Gas Hydrate Program Expedition 02 (NGHP-02). Marine and Petroleum Geology 108, 216-225.


The National Gas Hydrate Program Expedition 02 (NGHP-02) was designed to examine gas hydrate occurrences off the eastern margin of the Indian Peninsula. Twelve holes were logged with logging-while-drilling (LWD) tools and nine holes at five sites were cored in Area-B of NGHP-02. Five logging units were defined based on the characteristics in logging data responses. Distinctive Logging Units R1 and R2 characterized by high gamma ray log values and composed of quartz and biotite-rich medium sized sand grain units that act as gas hydrate resevoirs and correlated to strong seismic reflectors. Hydrate-bearing intervals can be identified by resistivity and sonic velocity logs and classified into pore-filling type, fracture-filling type, and a mixture of pore- and fracture-filling types based on borehole image characteristics. Pore-filling type gas hydrate is typically developed in the case where the depths of R1 and/or R2 is close to the seismic inferred bottom simulating reflector (BSR). Fracture-filling type hydrates associated the R1 section occur above the BSR associated with the anticline in Area-B. The occurrence of pore-filling and fracture-filling gas hydrate represent

different processes of hydrate formation related to the regional geological structure. The stratigraphic layered pore-filling gas hydrate occurrences are generated along often dipping sand layers, which are also conduits for methane-bearing fluid migrating from below the BSR in many settings. Fracture-filling type gas hydrate is an alternative mechanism for the occurrence of gas hydrate in mudstone-rich sediments above the BSR and found associated with the anticline in Area-B. This structural constraint of the hydrate-bearing fractures in the Area-B anticline suggest that the fracture dominated reservoirs possibly formed by anticlinal flexure, and the upward flow of methane-bearing fluids along porous sedimentary layers and the subsequent formation of pore-filling gas hydrate occurrences account for the range of gas hydrate accumulations discovered during NGHP-02.

Sánchez, A., Tuñón, J.A., Parras, D.J., Montejo, M., Lechuga, M.A., Ceprián, B., Soto, M., Luque, Á., 2019. MRS, EDXRF and GC–MS analysis for research on the ritual and funerary areas of Cerro de los Vientos (Baeza, Jaén, Spain). Native and Eastern Mediterranean influences. Journal of Archaeological Science: Reports 28, 102026.


This paper is about the results obtained from the physico-chemical analysis of the Orientalizing (7th century BC) archaeological materials retrieved from the ritual and funerary areas of the site Cerro de los Vientos (Baeza, Jaén, Spain). The samples under study are native tradition and Phoenician ceramic vessels, and beads of several colours. The analysis used Micro Raman Spectroscopy (MRS) with portable and laboratory equipments, Energy Dispersive X Ray Fluorescence (EDXRF) and Gas Chromatography-Mass Spectrometry (GC–MS). Joint use of these techniques allowed to examine the interaction between the native community of Cerro de los Vientos and the Eastern Mediterranean influence by populations of Phoenician origins.

Use of MRS and EDXRF helped identify the mineral and elemental composition of the decorations of the native and Phoenician ceramic vessels, and also of the red and blue beads. Hematite, goethite, amorphous carbon and graphite were recorded in the native pottery. Hematite and manganese oxide were recorded in the Phoenician pottery. The red beads were made of carnelian, a variety of chalcedony that is not found in the Iberian Peninsula. The blue beads were made of glass paste.

GC–MS contents analysis identified beeswax in most vessels, both native and Phoenician. The beeswax in native and Phoenician vessels from the area for the funerary feast and in the funerary urns laid in the graves leads to an interpretation in terms of hydromel consumption during feasts and offerings of honey in urns.

Santosh, M., Tsunogae, T., Yang, C.-X., Han, Y.-S., Hari, K.R., Prasanth, M.P.M., Uthup, S., 2020. The Bastar craton, central India: A window to Archean – Paleoproterozoic crustal evolution. Gondwana Research 79, 157-184.


The Bastar craton in central India, surrounded by cratonic blocks and Paleoproterozoic to Neoproterozoic orogenic belts, is a window to investigate the Archean-Paleoproterozoic crustal evolution and tectonic processes. Here we propose a new tectonic classification of the craton into the Western Bastar Craton (WBC), Eastern Bastar Craton (EBC), and the intervening Central Bastar

Orogen (CBO). We present petrologic, geochemical and zircon U-Pb, REE and Lu-Hf data from a suite of rocks from the CBO and along the eastern margin of the WBC Including: (1) volcanic successions comprising meta-andesite and fine-grained amphibolite, representing arc-related volcanics along a convergent margin; (2) ferruginous sandstone, in association with rhyolite, representing a volcano-sedimentary succession, deposited in an active trench; and (3) metamorphosed mafic-ultramafic suite including gabbro, pyroxenite and dunite invaded by trondhjemite representing the section of sub-arc mantle and arc root adjacent to a long-lasting subduction system. Petrologic studies indicate that the mafic-ultramafic suite crystallized from an island arc tholeiitic parental magma in a suprasubduction zone environment. The chondrite-normalized and primitive mantle normalized diagrams of the mafic and ultramafic rocks suggest derivation from MORB magma. The mixed characters from N-MORB to E-MORB of the studied samples are consistent with subduction modification of a MORB related magma, involving partial melting of the metasomatized mantle wedge. Our zircon U-Pb age data suggest that the cratonic nuclei was constructed as early as Paleoarchean. We present evidence for active subduction and arc magmatism through Mesoarchean to Neoarchean and early Paleoproterozoic, with the trench remaining open until at least 2.3 Ga. Two major crust building events are recognized in the Bastar craton: during Mesoarchean (recycled Paleoarchean subduction-related as well as juvenile/depleted mantle components) and Neoarchean (accretion of juvenile oceanic crust, arc magmatism including granite batholiths and related porphyry mineralization). The final cratonization occurred during latest Paleoproterozoic, followed by collisional assembly of the craton and its incorporation within the Peninsular Indian mosaic during Mesoproterozoic. In the global supercontinent context, the craton preserves the history of Ur, the earliest supercontinent, followed by the Paleo-Mesoproterozoic Columbia, as well as minor thermal imprints of the Neoproterozoic Rodinia and associated Grenvillian orogeny.

Saumya, S., Narasimhan, B., Singh, J., Yamamoto, H., Vij, J., Sakiyama, N., Kumar, P., 2019. Acquisition of logging-while-drilling (LWD) multipole acoustic log data during the India National Gas Hydrate Program (NGHP) Expedition 02. Marine and Petroleum Geology 108, 562-569.


Gas hydrates are ice-like crystalline minerals with high energy concentrations, which generally occur in deepwater environments, at low temperature and high pressure, usually close to the seafloor. Gas hydrate research wells are normally drilled riser-less, with multiple wells being drilled in rapid succession. Logging-while-drilling (LWD) is the preferred logging method as the borehole condition in such shallow formations deteriorates very rapidly after drilling. LWD helps minimize the time between drilling and logging. The LWD sonic measurement is key in such projects and is used typically for geomechanics and formation evaluation purposes.

The water-bearing sedimentary section within the shallow gas hydrate stability zone is often shale-rich, unconsolidated and the measured acoustic wave slowness is “extremely slow”, with shear slowness above 1400 μs/ft and bulk density of around 1.7 gm/cc. Quadrupole measurements are commonly used in the industry to log shear slowness with LWD tools in slow formations, where the shear slowness is slower than the borehole fluid slowness. However, it is very challenging to log shear slownesses with LWD sonic tool in these extremely slow formations, even with a quadrupole measurement. This paper details the challenges related to borehole acoustics logging in gas hydrate research wells, outlines the key technological enablers and gives an overview of the performance of LWD sonic tools during the National Gas Hydrate Program Expedition 02 (NGHP-02) in the offshore of India. It will spotlight the innovative approach followed to modify the LWD sonic acquisition and

processing to adapt to the extremely slow acoustic wave speeds, which facilitated recording LWD shear slowness up to approximately 1400 μs/ft.



Digital Rock Physics is a promising approach for achieving more, cheaper, and faster rock property characterization of digital images of rock samples. To successfully deliver on this potential, we must correctly interpret the digitally derived properties in the context of the limitations imposed by imaging constraints. To this end, we show that a combination of limited image resolution, a biased segmentation of images with coarse resolution, and a finite field of view of images, generated by the present micro-Computed Tomography (micro-CT) technology, leads to systematic underestimation of porosity (down to a factor of 0.5) and overestimation of permeability (up to a factor of 10) calculated using the Digital Rock Physics (DRP). We demonstrate these imaging limitations can be overcome by identifying good measures of image resolution and representative elementary volume and applying appropriate transforms. These transforms expand the operating envelop of DRP. Transforms for finite image resolution and limited field of view can be estimated directly from the micro-CT images. However, implementation of transforms related to errors in image segmentation require either a higher resolution image (e.g., nano-computed tomography, scanning electron microscopy) or laboratory measured constraints (Mercury injection capillary pressure, NMR porosity). Additionally, we suggest how insights from these transforms can be used to define operating envelopes and optimize imaging resolution and field of view to achieve more reliable results from digital rock characterization and simulations.

Schada von Borzyskowski, L., Severi, F., Krüger, K., Hermann, L., Gilardet, A., Sippel, F., Pommerenke, B., Claus, P., Cortina, N.S., Glatter, T., Zauner, S., Zarzycki, J., Fuchs, B.M., Bremer, E., Maier, U.G., Amann, R.I., Erb, T.J., 2019. Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle. Nature 575, 500-504.

https://doi.org/10.1038/s41586-019-1748-4

One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments. Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria, the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the β-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago. We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing—to our knowledge—the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full

turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.

Schoenemann, B., Poschmann, M., Clarkson, E.N.K., 2019. Insights into the 400 million-year-old eyes of giant sea scorpions (Eurypterida) suggest the structure of Palaeozoic compound eyes. Scientific Reports 9, 17797.

https://doi.org/10.1038/s41598-019-53590-8

Sea scorpions (Eurypterida, Chelicerata) of the Lower Devonian (~400 Mya) lived as large, aquatic predators. The structure of modern chelicerate eyes is very different from that of mandibulate compound eyes [Mandibulata: Crustacea and Tracheata (Hexapoda, such as insects, and Myriapoda)]. Here we show that the visual system of Lower Devonian (~400 Mya) eurypterids closely matches that of xiphosurans (Xiphosura, Chelicerata). Modern representatives of this group, the horseshoe crabs (Limulidae), have cuticular lens cylinders and usually also an eccentric cell in their sensory apparatus. This strongly suggests that the xiphosuran/eurypterid compound eye is a plesiomorphic structure with respect to the Chelicerata, and probably ancestral to that of Euchelicerata, including Eurypterida, Arachnida and Xiphosura. This is supported by the fact that some Palaeozoic scorpions also possessed compound eyes similar to those of eurypterids. Accordingly, edge enhancement (lateral inhibition), organised by the eccentric cell, most useful in scattered light-conditions, may be a very old mechanism, while the single-lens system of arachnids is possibly an adaptation to a terrestrial life-style.

Senik, S.V., Psurtseva, N.V., Shavarda, A.L., Kotlova, E.R., 2019. Role of lipids in the thermal plasticity of basidial fungus Favolaschia manipularis. Canadian Journal of Microbiology 65, 870-879.

https://doi.org/10.1139/cjm-2019-0284

In this study, we examined the lipid composition of two strains of the tropical basidiomycete Favolaschia manipularis (Berk.) Teng, which differ in their adaptive potential to high (35 °C) and low (5 °C) temperatures. The results suggest that adaptation to extreme temperatures involves a change in the molecular composition of sterols, in addition to other well-known mechanisms of regulating membrane thickness and fluidity, such as changes in the lipid unsaturation and in the proportion of bilayer- and non-bilayer-forming lipids. It was demonstrated for the first time that adaptation to high temperature stress in fungi is accompanied by the accumulation of 9(11)-dehydroergosterol and ergosterol peroxide. Furthermore, increased thermal plasticity correlates with high storage lipid (triglycerides) content, accumulation of phosphatidic acid in the membrane, and an equal proportion of bilayer and non-bilayer lipids in the membrane.

Sepideh, K., Lotfollahi, M.N., Shahrabadi, A., 2019. Asphaltene adsorption using nanoparticles with different surface chemistry: Equilibrium and thermodynamics studies. Petroleum Chemistry 59, 1201-1206.

https://doi.org/10.1134/S0965544119110124

This study investigates the equilibrium adsorption of asphaltene onto several nanoparticles (NiO, MgO, Fe3O4) with different surface chemistry at various temperatures by UV-Vis spectroscopy. The NiO had acidic surface; however the MgO and Fe3O4 had basic and amphoteric surfaces respectively, which were determined by titration method. The isotherm data of the nanoparticles were best modeled by Langmuir model that indicated monolayer asphaltene adsorption onto the nanoparticles. The maximum asphaltene adsorption capacities of the nanoparticles were obtained at minimum temperature (25°C) in the range of 0.6364–1.0545 mg/m2 that decreased in the order of NiO > MgO > Fe3O4. The results confirm the potential application of nanoparticles with acidic surface for adsorption and removing of asphaltene. Moreover, the thermodynamic parameters at different temperatures showed that the adsorption of asphaltene onto the nanoparticles was spontaneous (ΔG0 < 0), exothermic (ΔH0 < 0) and physical (2.1< |ΔH0| <20.9 kJ/mol).

Shang, Z., Dong, L., Niu, L., Shi, H., 2019. Adsorption of methane, nitrogen, and carbon dioxide in atomic-scale fractal nanopores by Monte Carlo simulation I: Single-component adsorption. Energy & Fuels 33, 10457-10475.


The atomic-scale surface fractal, which can notably affect gas adsorption, is a prominent form of geometric heterogeneity at the surfaces of the pore structure of shale. Systematically evaluating the effect of the atomic-scale surface fractal on gas adsorption remains an open research question. In this study, we investigated the single-component adsorption of methane, nitrogen, and carbon dioxide in fractal shale nanopores at 298 K by Monte Carlo simulations in the grand canonical ensemble. We carved out the atomistic nanopore models by fractal surfaces created using the diamond-square algorithm with the surface fractal dimension ranging from 2 to 2.9. We evaluated the variation in the adsorption energy, the absolute and excess adsorbed density, and the adsorption layer density with the surface fractal dimension, which indicates that the atomic-scale surface fractal is an unfavorable factor for the single-component adsorption of methane, nitrogen, and carbon dioxide. The findings may enhance our understanding of the mechanism for heterogeneous gas adsorption in shale.

Shao, D., Zhang, T., Ko, L.T., Li, Y., Yan, J., Zhang, L., Luo, H., Qiao, B., 2020. Experimental investigation of oil generation, retention, and expulsion within Type II kerogen-dominated marine shales: Insights from gold-tube nonhydrous pyrolysis of Barnett and Woodford Shales using miniature core plugs. International Journal of Coal Geology 217, 103337.


Although oil retention has recently emerged as a key topic of unconventional-shale resource assessment, oil-retention and expulsion controls in organic-rich shales during thermal maturation remain poorly constrained. This study presents an experimental comparison of oil generation, retention, and expulsion in two immature, Type II kerogen-dominated marine shales, the Mississippian Barnett Shale and the Upper Devonian-Lower Mississippian Woodford Shale, mainly with respect to the combined effects of the organic macerals and rock fabric involved. In both cases, miniature core plugs drilled from the given samples were isothermally pyrolyzed at 130 to 425 °C for 72 h under a confining pressure of 68 MPa during gold-tube nonhydrous pyrolysis, corresponding to the thermally immature, early stage of the oil window, the main stage of the oil window, the late

stage of the oil window, the main stage of oil cracking to wet gas, and the late stage of oil cracking. Yields of generated oil, retained oil, and expelled oil for the two studied samples were systematically quantified on the basis of mass-balance calculation of measured oil and gas yields, as well as Rock-Eval analyses on pyrolyzed subsamples.

Through the six stages of petroleum formation investigated, the principal difference in oil generation was observed in the two studied samples, with approximately 38 to 68% greater yields of generated oil (equivalent to ~130 mg oil/g TOCo) for the Woodford Shale when it evolved into the main and late stages of the oil window. These elevated yields of generated oil for the Woodford Shale were compensated for by additional oil generation resulting from conversion of abundant Type I kerogen-like algae such as Tasmanites and Leiosphaeridia, which lag in onset and have a shorter period of petroleum generation upon maturation. As a response to the difference in oil generation, oil retention was found to be significantly enhanced for the Woodford Shale at equivalent stages, with 0.2 to 1.7 times more free oil (equivalent to 24–105 mg oil/g TOCo) and 0.7 to 3.9 times more sorbed oil (equivalent to 58–76 mg oil/g TOCo) being retained than that of the Barnett Shale, although this effect was not pronounced for oil expulsion. In contrast to the Barnett Shale, relatively low expelled oil yields and expulsion efficiencies both indicate highly limited oil expulsion in the Woodford Shale, implying that the Woodford Shale, whose mineral composition and lithofacies are similar to those of the Barnett Shale, may have a relatively low permeability rock fabric to prevent oil from being expelled. Furthermore, not only significantly higher oil-saturation index (OSI) values but also a wider range of maturity at which the oil crossover effect (OSI > 100 mg/g TOC) occurs is expected for the Woodford Shale when extrapolation to a geological setting occurs. These data suggest that the presence of abundant Type I kerogen-like algae and relatively low permeability rock fabric in the Woodford Shale are critical to significant oil retention during oil generation and expulsion, which jointly raise the possibility of potential commercial shale oil within Type II kerogen-dominated marine shales.

Sharma, S., Steuer, R., 2019. Modelling microbial communities using biochemical resource allocation analysis. Journal of The Royal Society Interface 16, 20190474.

https://doi.org/10.1098/rsif.2019.0474

To understand the functioning and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, a large chasm between ecologically motivated descriptions of microbial growth used in many current ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed in the context of systems and synthetic biology. Here, we seek to demonstrate how resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parametrization. In particular, recent work on quantitative resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. These models go beyond Michaelis–Menten and Monod-type growth models, and are capable of accounting for emergent properties that underlie the remarkable plasticity of microbial growth. We outline the utility and advantages of using biochemical resource allocation models by considering a coarse-grained model of cyanobacterial growth and demonstrate how the model allows us to address specific questions of relevance for the simulation of marine microbial ecosystems, including the physiological acclimation of protein expression to different environments, the description of co-limitation by several nutrients and the differential use of alternative nutrient sources, as well as the

description of metabolic diversity based on our increasing knowledge about quantitative cell physiology.



Plants are direct recorders of the environmental conditions in which they were growing through their carbon assimilation. Both δ13Cleaf (measured C isotopic composition of the leaf) and Δleaf (isotopic discrimination from δ13Catm by the leaf) values have been proposed to reflect a variety of environmental conditions including MAT, MAP, latitude, elevation, [CO2], and δ13Catm. Herein, we examine three sets of data from gymnosperms with long fossil records as well as selected co-occurring angiosperms to compare responses to potential environmental controls. The first dataset comprises species growing across a wide array of climatic and environmental conditions to examine MAT, MAP, latitude, and elevation. Among those potential environmental factors, none exhibits a strong control on either δ13Cleaf or Δleaf at the family, genus, or species level for either the focal gymnosperms or most of the co-occurring angiosperms. This result holds whether temperature or precipitation are considered annually or seasonally. Plant meta-analyses that have suggested a strong relationship between MAP and δ13Cleaf or Δleaf can instead be interpreted as reflecting constant Δleaf for individual species over their environmental occurrence ranges where individual ecosystems are made up of various species at different points along their individual MAP tolerance. The second dataset comes from an array of species all growing under the same environmental conditions. While differences in δ13Cleaf or Δleaf are small at the family level, at the genus and species level variation is much larger. This suggests that for any paleo-proxy reconstruction, accurate plant identification is critical to selecting the appropriate Δleaf. It also may indicate that there is an evolutionary component to measured Δleaf values, with large differences potentially between early-divergent and derived lineages. The third dataset is derived from herbarium collections of species that span the period of Industrialization (1850-present). During this time period CO2 levels have increased by ~50% and δ13Catm has shifted by >2‰ due to the burning of isotopically more negative fossil fuels. All of the historical records show that plants shifted their δ13Cleaf value, tracking the δ13Catm changes, but they did not change their Δleaf values. This contrasts strongly with some experimental results based on fast-growing herbaceous angiosperms and suggests either that there are fundamental differences between woody and herbaceous plants and/or that gymnosperms respond differently to increased CO2 than angiosperms. Finally, a brief case study is presented that examines how water use efficiency (represented by ci/ca) changed in response to elevated atmospheric CO2 levels in the Eocene to Miocene. Both Thuja and Metasequoia substantially increase their ci/ca ratios during the highest CO2 levels in the Eocene and decreased them in response to falling atmospheric CO2 during the Miocene. This suggests that the compiled Δ leaf values described herein can be used to improve a variety of paleo-proxies for atmospheric CO2 levels and for plant responses to changing atmospheric stressors.

Shen, C., Zhao, J., Ren, L., Fan, Y., 2019. A new fracturing sweet spot identification method in Longmaxi Formation of Sichuan Basin, SW China. Journal of Natural Gas Geoscience 4, 279-286.


The key to obtaining economic productivity on shale gas reservoir stimulation is to identify the fracturing sweet spots. This paper considers several factors on stimulation such as layered property, brittle minerals contents, and natural weak plane as featured in Wufeng Formation-Longmaxi Formation in Sichuan Basin. It is proposed that the layered and fracture index, brittleness index, and fracture network probability index be utilized so as to establish a method on identifying fracturing sweet spot based on shale facies. The researchers have concluded that shale reservoir, with layered and fracture index ranging from 0.55 to 0.6, brittleness index ranging from 0.45 to 0.5, and fracture network probability index measuring between 0.6 and 1.0, be classified as the fracturing sweet spot. The said qualifications have preponderant stimulation potential and efficient network-fracturing due to visible layered property, varied brittle minerals, and developed packed fractures. It is also concluded that shale with visible layered property, high carbonate proportion, and moderate development of packed fractures could obtain better stimulation. The conclusion from this paper agrees with the result achieved that of micro-seismic monitoring and production profile. The method could be the theoretical foundation and live guidance for providing strategy and design scheme for fracturing.



The amount and biodegradability of oil-degrading bacteria in seawater should be augmented to improve the biodegradation of marine petroleum hydrocarbons. This study investigated the degradation of petroleum-degrading bacteria (P1) with biosurfactant-producing bacteria (B2) and its mechanism. Two groups of experiments that consist of P1 with and without B2 were designed. The degradation performance and surface characteristics of the bacteria and the degradation path of diesel were studied. The degradation rate in the group of P1 with B2 was 82.65%, which was higher than that without B2, after 12 days. The analysis of surface characteristics showed that a high hydrophobicity enabled diesel to be accessible to cells. Meanwhile, the addition of B2 increased the contact area between bacteria and diesel, which was favorable to bioaugmentation degradation. The diesel degradation paths included surface adsorption, cell uptake, and biodegradation. The first step of diesel degradation was a rapid surface adsorption followed by cell uptake. The velocities of the removal rate of diesel by biodegradation and cell uptake in the group of P1 with B2 were higher than those without B2.

Shi, X., Wang, S., Jasbi, P., Turner, C., Hrovat, J., Wei, Y., Liu, J., Gu, H., 2019. Database-assisted globally optimized targeted mass spectrometry (dGOT-MS): Broad and reliable metabolomics analysis with enhanced identification. Analytical Chemistry 91.


Targeted mass spectrometry (MS) is an important measurement approach in metabolomics with strong analytical performance, given its specificity, sensitivity, and quantitative capacity. However, traditional targeted-MS relies heavily on chemical standards for the development of various detection panels; thus, its metabolite coverage is often limited to those well-known and commercially available compounds. To address this fundamental gap, we previously developed a

novel approach [H. Gu et al. Anal. Chem. 2015, 87, 12355−12362], globally optimized targeted (GOT)-MS, which enables reliable metabolic analysis with broad coverage using a single triple quadrupole instrument. In the present study, we further developed and optimized an innovative targeted MS approach, database-assisted globally optimized targeted (dGOT)-MS, which utilizes the HMDB and METLIN databases to significantly improve both identification and metabolite coverage. As it is well-known, these metabolomics databases have a comprehensive collection of metabolites and their tandem MS spectra; therefore, in this study, multiple reaction monitoring transitions (MRMs) were directly obtained from the databases and, after optimizing MS parameters for those MRMs, 927 metabolites were measured from a plasma aqueous extract sample with high reliability by dGOT-MS. Of these, 310 were confirmed using pure chemical standards while the rest were annotated by identification level using database entries. Furthermore, using breast cancer diagnosis as a proof-of-principle metabolomics application, we showed dGOT-MS to significantly outperform a traditional large-scale targeted MS assay for potential biomarker discovery. In principle, dGOT-MS is able to cover all metabolites (including lipids) that have been characterized in these comprehensive metabolomics databases from various types of biological samples. Therefore, dGOT-MS opens a novel avenue for MS measurements and may play an important role in many future metabolomics studies.

Shi, Y.-h., Liang, Q.-y., Yang, J.-p., Yuan, Q.-m., Wu, X.-m., Kong, L., 2019. Stability analysis of submarine slopes in the area of the test production of gas hydrate in the South China Sea. China Geology 2, 276-286.


ABSTRACT In this paper, the mechanical properties of gas hydrate-bearing sediments (GHBS) were summarized and the instability mechanism of submarine hydrate-bearing slope (SHBS) was analyzed under the background of the test production of gas hydrate in the northern part of the South China Sea. The strength reduction finite element method (SRFEM) was introduced to the stability analysis of submarine slopes for the safety of the test production. Two schemes were designed to determine the physical and mechanical parameters of four target wells. Through the division of the hydrate dissociation region and the design of four working conditions, the range and degree of hydrate dissociation at different stages during the test production were simulated. Based on the software ABAQUS, 37 FEM models of SHBS were set up to analyze and assess the stability of the submarine slopes in the area of the test production. Necessary information such as safety factors, deformation, and displacement were obtained at different stages and under different working conditions. According to the calculation results, the submarine slope area is stable before the test production, and the safety factors almost remains the same during and after the test production. All these indicate that the test production has no obvious influence on the area of the test production and the submarine slopes in the area are stable during and after the test production.

Shi, Y.-K., Huang, H., Shen, Z.-H., 2019. New insights for ancient foraminifera through 3D visuals of fusulinids. Palaeoworld 28, 478-486.


Fusulinids are larger benthic foraminifera of late Paleozoic and index fossils for Permo-Carboniferous strata. The traditional methods to examine their internal structures are through

ground thin sections, which however caused lots of ambiguities regarding the morphological diagnostics and taxonomic identification.

In recent years, new technique of high resolution X-ray computed tomography sheds light on the microfossil examination and we had fusulinid individuals successfully processed with this innovative approach. Here we present the results of 19 Pseudofusulina specimens, including high resolution images and rendered three-dimensional (3D) visuals of the important internal structures, to unwrap more details of fusulinid morphology. This is the first time the full 3D visuals of fusulinid interiors were constructed and exhibited. Previous understandings on fusulinid basic morphology, such as proloculus, chamber development, are precisely described with 3D illustration; cuniculi and phrenotheca are discovered regularly among the specimens and therefore are not suggested to be diagnostic features of taxonomic splitting; test and proloculus morphology divergences caused by section orientation are captured. With assistance of high resolution CT technique, fusulinid morphology, especially internal structures, is much easier to acquire, understand, and exhibit, despite the critical limitation that only the fusulinid samples buried with terrigenous clasts, such as those from calcareous mudstone or argillaceous limestone, could be successfully scanned.

Shorten, C.M., Fitzgerald, P.G., 2019. Post-orogenic thermal history and exhumation of the northern Appalachian Basin: Low-temperature thermochronologic constraints. Basin Research 31, 1017-1039.

https://doi.org/10.1111/bre.12354

Apatite fission track (AFT) thermochronology and (U Th)/He (AHe) dating, combined with ‐ ‐paleothermometers and independent geologic constraints, are used to model the thermal history of Devonian Catskill delta wedge strata. The timing and rates of cooling determines the likely post‐orogenic exhumation history of the northern Appalachian Foreland Basin (NAB) in New York and Pennsylvania. AFT ages generally young from west to east, decreasing from ~185 to 120 Ma. AHe single grain ages range from ~188 to 116 Ma. Models show that this part of the Appalachian ‐foreland basin experienced a non uniform, multi stage cooling history. Cooling rates vary over time, ‐ ‐~1–2 °C/Myr in the Early Jurassic to Early Cretaceous, ~0.15–0.25 °C/Myr from the Early Cretaceous to Late Cenozoic, and ~1–2 °C/Myr beginning in the Miocene. Our results from the Mesozoic are broadly consistent with earlier studies, but with the integration of multiple thermochronometers and multi kinetic annealing algorithms in newer inverse thermal modeling programs, we constrain a ‐Late Cenozoic increase in cooling which had been previously enigmatic in eastern U.S. low‐temperature thermochronology datasets. Multi stage cooling and exhumation of the NAB is driven ‐by post orogenic basin inversion and catchment drainage reorganization, in response to changes in ‐base level due to rifting, plus isostatic and dynamic topographic processes modified by flexure over the long (~200 Myr) post orogenic period. This study compliments other regional exhumation data‐ ‐sets, while constraining the timing of post orogenic cooling and exhumation in the NAB and ‐contributing important insights on the post orogenic development and inversion of foreland basins ‐along passive margins.

Shui, H., Zhao, L., Sun, J., Shui, T., Pan, C., Wang, Z., Lei, Z., Ren, S., Kang, S., Xu, C.C., 2020. Hydro-liquefaction of asphaltene from a lignite for potential jet fuel. Fuel 262, 116435.


Hydro-liquefaction of an asphaltene from thermal dissolution of Xinlinguole lignite (XLAS) was carried out, and the effects of catalyst, temperature and reaction time on oil yield and cyclanes content in oil for the potential jet fuel were probed in this study. Comparing the hydrogenation activities of three catalysts i.e. Cu-Ni/γ-Al2O3, Ni/ZSM-5 and Ni-Mo-S/γ-Al2O3, it was found that Ni-Mo-S/γ-Al2O3 was the most beneficial for jet fuel production from coal liquefied oil due to it contained a continuous distribution of weaker to stronger acidic sites. It gave the highest oil yield of 68.8%, and cyclanes content of 20.5% in the oil, which displayed the highest hydrogenation activity for arenes saturated hydrogenating among the three catalysts used in the hydro-liquefactions of XLAS at 360 °C for 90 min. For Cu-Ni/γ-Al2O3, it only contained weak acidic sites therefore it gave the lowest saturated hydrogenating activity. With rising of temperature, oil yield increased, but cyclanes content in oil decreased in the hydro-liquefactions of XLAS under Ni-Mo-S/γ-Al2O3 catalyst. The highest content of cyclanes (29.3%) in oil was obtained at 280 °C for 90 min. Reaction time remarkably affected cyclanes content in oil. With the reaction time prolonging from 30 to 60 min, oil yield and cyclanes content in oil increased. Further prolonging reaction time to 90 min, oil yield hardly increased, but cyclanes content in oil decreased from 23.6% to 20.5% at 360 °C with Ni-Mo-S/γ-Al2O3 catalyst. Some oxygen-containing compounds (OCs) may convert into cyclanes by hydro-deoxygenation (HDO) with increasing of reaction time.

Shukla, K.M., Collett, T.S., Kumar, P., Yadav, U.S., Boswell, R., Frye, M., Riedel, M., Kaur, I., Vishwanath, K., 2019. National Gas Hydrate Program expedition 02: Identification of gas hydrate prospects in the Krishna-Godavari Basin, offshore India. Marine and Petroleum Geology 108, 167-184.


After completing the first expedition of India's National Gas Hydrate Program (NGHP-01) in 2006, it was concluded that for the next expedition (National Gas Hydrate Program 02; NGHP-02), a new drill site review effort should focus on identifying potential deep-water offshore gas hydrate accumulations in sand dominated depositional environments. Therefore, geological and geophysical data analysis and 3D seismic data interpretation along with associated seismic modeling were carried out in three areas of the Krishna-Godavari Basin: Areas B, C, and E. Conventional petroleum exploration approaches of seismic amplitude evaluation were adapted to prospect for potentially sand-rich depositional systems within the gas hydrate stability zone. Subsequently, these prospective areas were further assessed through the geological and geophysical evaluation of depositional setting, gas sources, and gas migration pathways. In Area B, prospecting focused on a large anticlinal structure with a prominent bottom-simulating reflector and several key horizons that indicated evidence for potential sand-hosted hydrate occurrences. In Area C, the prospects were distributed throughout various settings within a very large deep-water channel-levee-fan system with complex indications of potential gas hydrate occurrence in sand-prone seismic facies. In Area E, prospects were associated with high amplitude events within inferred channel-levee sequences. Based on the pre-expedition/onboard drill-site evaluation, the 22 most promising sites in the Krishna-Godavari Basin were identified and prioritized to investigate and delineate a total of 17 identified gas hydrate prospects. This paper describes the geo-scientific studies carried out prior to NGHP-02 for site identification, evaluation and prioritization. An important outcome of this study is the identification of two potentially producible gas hydrate systems inferred to host significant quantities of gas hydrate in stratigraphic-structural traps.

Shukla, K.M., Kumar, P., Yadav, U.S., 2019. Gas hydrate reservoir identification, delineation, and characterization in the Krishna-Godavari basin using subsurface geologic and geophysical data from the National Gas Hydrate Program 02 Expedition, offshore India. Marine and Petroleum Geology 108, 185-205.


During the National Gas Hydrate Program Expedition-02 (NGHP-02), logging while drilling, conventional coring and pressure coring, wire-line logging, vertical seismic profiling and formation pressure measurements were carried out in deep water portions of the Krishna-Godavari (K-G) and Mahanadi Basins along the eastern continental margin of India. A total of 42 research holes were completed for comprehensive data collection and measurements related to gas hydrate reservoir and host sediments properties with an objective to identify producible gas hydrate in sand-rich reservoirs that would be suitable for a future pilot production test. Shipboard and post cruise evaluation of physical properties measurements, pressure core dissociation studies and gas analysis of recovered core samples have confirmed the occurrence of sand hosted gas hydrate deposits in three operational areas named during NGHP-02 as Area B, Area C and Area E in the deep-water portion of the K-G Basin. The energy resource potential of the discovered gas hydrate deposits in the K-G Basin depends on many factors, including the quantity of available gas trapped as gas hydrate in the basin. Therefore, this study was undertaken to identify, characterize and delineate the discovered and confirmed gas hydrate prospects in the K-G Basin. Based on the integrated analysis of regional seismic data and NGHP-02 acquired borehole data, a total of 8 sand-rich reservoir constrained gas hydrate prospects have been identified and mapped in the K-G Basin (Areas B, C, and E) as described in this report.


http://mbio.asm.org/content/10/6/e02128-19.abstract

Abstract: The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia. Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C.

psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.

Importance: CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence.

Silva, R.L., Duarte, L.V., Wach, G.D., Morrison, N., Campbell, T., 2020. Oceanic organic carbon as a possible first-order control on the carbon cycle during the Bathonian–Callovian. Global and Planetary Change 184, 103058.


Oceans are the largest, readily exchangeable, superficial carbon reservoir; a current challenge in investigating past and present environments and predict future evolution relates to the role of oceanic carbon in regulating Earths' carbon cycle and climate.

At least one paired δ13Ccarb-TOC decoupling event is noted in the Late Bathonian–Early Callovian. Provokingly, we suggest that this decoupling event and other carbon isotopic events in the Bathonian–Callovian resulted from the addition and removal of carbon from the oceanic organic carbon (OOC) reservoir, likely dominated by dissolved and fine particulate oceanic organic carbon. The decoupling event is characterised by a mainly invariant δ13CTOC record and increasingly more positive δ13Ccarb values. The δ13Ccarb-TOC decoupling is tentatively explained by the expansion of the OOC reservoir, which increased the residence time of carbon in the oceans and buffered (slow equilibrium) δ13COOC (approximated by δ13CTOC) to changes in δ13C of oceanic inorganic carbon, comprised mainly of dissolved inorganic carbon (approximated by δ13Ccarb). Reconversion of OOC to CO2 may have resulted in negative δ13C excursions and increased atmospheric pCO2, whereas the change from accumulation of OOC to export of organic carbon to sediments may have resulted in positive δ13C excursions and widespread accumulation of organic matter. It is speculated that other small-scale (~ 1‰) δ13C excursions in the Mesozoic record may have resulted from similar episodes of OOC accumulation and oxidation.

Our study calls attention to the potential of the OOC reservoir to act as a critical driver for planetary-scale changes over short geological time intervals.

Singh, R., Ryu, J., Kim, S.W., 2019. Microbial consortia including methanotrophs: some benefits of living together. Journal of Microbiology 57, 939-952.

https://doi.org/10.1007/s12275-019-9328-8

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

Sivadon, P., Barnier, C., Urios, L., Grimaud, R., 2019. Biofilm formation as a microbial strategy to assimilate particulate substrates. Environmental Microbiology Reports 11, 749-764.

https://doi.org/10.1111/1758-2229.12785

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man made ‐organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle degrading biofilms are widespread and have been observed in aquatic and terrestrial ‐natural ecosystems, in polluted and man driven environments and in the digestive tracts of animals. ‐They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non dissolved organic carbon, and considers the advantage ‐provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Slater, J.D., Chronopoulos, T., Panesar, R.S., Fitzgerald, F.D., Garcia, M., 2019. Review and techno-economic assessment of fuel cell technologies with CO2 capture. International Journal of Greenhouse Gas Control 91, 102818.


The concept of using Fuel Cells (FCs) within large scale power generation cycles for CO2 capture has been studied over the last decade. Two types of FCs, Solid Oxide Fuel Cells (SOFCs) and Molten Carbonate Fuel Cells (MCFCs) have emerged as promising CO2 capture systems, with the added advantage of additional power production. Although promising, neither SOFCs nor MCFCs are commercially available for CO2 capture applications, primarily due to low technological maturity, lack of large demonstration projects, and significant associated costs.

In this work, the aim is to provide a comprehensive literature review of Fuel Cell technologies with CO2 Capture and a techno-economic analysis of five selected cases utilising SOFCs and MCFCs as CO2 capture systems in power plants. Economic parameters were homogenised to enable a fair comparison between the technologies. Results show that Cases 1 and 5 which consider MCFCs as CO2 concentrator’s in Natural gas and super critical pulverised coal cycles respectively give the best LCOE performance. The LCOE is comparable to current state-of-the-art CO2 capture technologies applied to large-scale power plants.

Smith, T.P., Thomas, T.J.H., García-Carreras, B., Sal, S., Yvon-Durocher, G., Bell, T., Pawar, S., 2019. Community-level respiration of prokaryotic microbes may rise with global warming. Nature Communications 10, 5124.

https://doi.org/10.1038/s41467-019-13109-1

Understanding how the metabolic rates of prokaryotes respond to temperature is fundamental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima ≲45°C), but not thermophiles (≳45°C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Because climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, biomass-specific CO2 production, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.

Smits, P., Finnegan, S., 2019. How predictable is extinction? Forecasting species survival at million-year timescales. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190392.

https://doi.org/10.1098/rstb.2019.0392

A tenet of conservation palaeobiology is that knowledge of past extinction patterns can help us to better predict future extinctions. Although the future is unobservable, we can test the strength of this proposition by asking how well models conditioned on past observations would have predicted subsequent extinction events at different points in the geological past. To answer this question, we analyse the well-sampled fossil record of Cenozoic planktonic microfossil taxa (Foramanifera, Radiolaria, diatoms and calcareous nanoplankton). We examine how extinction probability varies over time as a function of species age, time of observation, current geographical range, change in geographical range, climate state and change in climate state. Our models have a 70–80%

probability of correctly forecasting the rank order of extinction risk for a random out-of-sample species pair, implying that determinants of extinction risk have varied only modestly through time. We find that models which include either historical covariates or account for variation in covariate effects over time yield equivalent forecasts, but a model including both is overfit and yields biased forecasts. An important caveat is that human impacts may substantially disrupt range-risk dynamics so that the future will be less predictable than it has been in the past.



Polycyclic aromatic hydrocarbons (PAH) contained in creosote oil are particularly difficult to remove from the soil environment. Their hydrophobic character and low bioavailability to soil microorganisms affects their rate of biodegradation. This study was performed on samples of soil that were (for over forty years) subjected to contamination with creosote oil, and their metagenome and physicochemical properties were characterized. Moreover, the study was undertaken to evaluate the biodegradation of PAHs by autochthonous consortia as well as by selected bacteria strains isolated from long-term contaminated industrial soil. From among the isolated microorganisms, the most effective in biodegrading the contaminants were the strains Pseudomonas mendocina and Brevundimonas olei. They were able to degrade more than 60% of the total content of PAHs during a 28-day test. The biodegradation of these compounds using AT7 dispersant was enhanced only by Serratia marcescens strain. Moreover, the addition of AT7 improved the effectiveness of fluorene and acenaphthene biodegradation by Serratia marcescens 6-fold. Our results indicated that long-term contact with aromatic compounds induced the bacterial strains to use the PAHs as a source of carbon and energy. We observed that supplementation with surfactants does not increase the efficiency of hydrocarbon biodegradation.



Petroleum refineries and petrochemical plants are major CO2 sources, however, they are also significant capital and employment assets that are unlikely to be replaced in the near term. As a result, nations and states that are interested in reducing the carbon intensity of their economies will need to find ways to reduce the emissions of their existing industrial capacity. Industrial carbon capture provides one potential mechanism for reducing the carbon intensity of existing industrial facilities, however, an economically feasible capture system requires that the captured CO2 be integrated into a system of transport and storage with income generated either through tax credits, enhanced oil recovery (EOR), or both. Here, we present a cash-flow model of an integrated system with industrial capture, pipeline transport, and EOR, and we parameterize the model with data from Louisiana. Given a $50/bbl oil price, an integrated capture, transport and EOR system that uses ethylene oxide production, ammonia production, or natural gas processing as sources is predicted to have a net present value of about $500 million; hydrogen-based capture has a cash flow of −$214

given the same assumptions. Further, we find that the recent 45Q Tax Credit expansion has a positive impact on the cash flow of the system but does not change the overall profitability of the systems under the specified assumptions such that without the tax credits natural gas processing, ammonia production and ethylene oxide production-based capture systems remain cost-effective, while hydrogen-based capture remains unprofitable with or without the tax credit.

Snyder, D.T., Panczyk, E., Stiving, A.Q., Gilbert, J.D., Somogyi, A., Kaplan, D., Wysocki, V., 2019. Design and performance of a second-generation surface-induced dissociation cell for Fourier transform ion cyclotron resonance mass spectrometry of native protein complexes. Analytical Chemistry 91, 14049-14057.


A second-generation (“Gen 2”) device capable of surface-induced dissociation (SID) and collision-induced dissociation (CID) for Fourier transform ion cyclotron resonance mass spectrometry of protein complexes has been designed, simulated, fabricated, and experimentally compared to a first-generation device (“Gen 1”). The primary goals of the redesign were to (1) simplify SID by reducing the number of electrodes, (2) increase CID and SID sensitivity by lengthening the collision cell, and (3) increase the mass range of the device for analysis of larger multimeric proteins, all while maintaining the normal instrument configuration and operation. Compared to Gen 1, Gen 2 exhibits an approximately 10× increase in sensitivity in flythrough mode, 7× increase in CID sensitivity for protonated leucine enkephalin (m/z 556), and 14× increase of CID sensitivity of 53 kDa streptavidin tetramer. It also approximately doubles the useful mass range (from m/z 8000 to m/z 15 000) using a rectilinear ion trap with a smaller inscribed radius or triples it (to m/z 22 000) using a hexapole collision cell and yields a 3–10× increase in SID sensitivity. We demonstrate the increased mass range and sensitivity on a variety of model molecules spanning nearly 3 orders of magnitude in absolute mass and present examples where the high resolution of the FT-ICR is advantageous for deconvoluting overlapping SID fragments.

Snyder, D.T., Szalwinski, L.J., St. John, Z., Cooks, R.G., 2019. Two-dimensional tandem mass spectrometry in a single scan on a linear quadrupole ion trap. Analytical Chemistry 91, 13752-13762.


A two-dimensional tandem mass spectrometry (2D MS/MS) scan has been developed for the linear quadrupole ion trap. Precursor ions are mass-selectively excited using a nonlinear ac frequency sweep at constant rf voltage, while simultaneously, all product ions of the excited precursor ions are ejected from the ion trap using a broad-band waveform. The fragmentation time of the precursor ions correlates with the precursor m/z value (the first mass dimension) and also with the ejection time of the product ions, allowing the correlation between precursor and product ions. Additionally, the second mass dimension (product ions’ m/z values) is recovered through fast Fourier transform of each mass spectral peak, revealing either intentionally introduced “frequency tags” or the product ion micropacket frequencies, both of which can be converted to product ion m/z through the classical Mathieu parameters, thereby revealing a product ion mass spectrum for every precursor ion without prior isolation. We demonstrate the utility of this method for analyzing a broad range of structurally related precursor ions, including chemical warfare agent simulants,

fentanyls and other opioids, amphetamines, cathinones, antihistamines, and tetracyclic antidepressants.

Snyder, S.M., Pulster, E.L., Murawski, S.A., 2019. Associations between chronic exposure to polycyclic aromatic hydrocarbons and health indices in Gulf of Mexico tilefish (Lopholatilus chamaeleonticeps) post Deepwater Horizon. Environmental Toxicology and Chemistry 38, 2659-2671.


A time series of polycyclic aromatic hydrocarbon (PAH) data was collected for Gulf of Mexico demersal fishes in the years following the Deepwater Horizon oil spill (2012–2017). Tilefish (Lopholatilus chamaeleonticeps) were sampled via demersal longline at repeat stations in the northern Gulf of Mexico in 2012 to 2015 and 2017. Bile samples (n = 256) were analyzed via high‐performance liquid chromatography with fluorescence detection for PAH metabolites as a biomarker of exposure to PAHs. Liver tissues (n = 230) were analyzed for accumulation of PAHs and alkylated homologs via quick, easy, cheap, effective, rugged, and safe (QuEChERS) extractions and gas chromatography–tandem mass spectrometry quantification. Over the 6 yr time series, exposure ‐to petrogenic PAHs increased by an average of 178%, correlating with an average 22% decline in Fulton's condition factor. The decline in Fulton's condition factor was positively correlated with a 53% decline in percentage of liver lipid. There was no accumulation of PAHs in liver tissue over time. Together, these results suggest that increasing and chronic PAH exposure and metabolism may be taxing the energy budgets of tilefish, particularly adult females, with potentially negative impacts on fitness.

Soares-Castro, P., Yadav, T.C., Viggor, S., Kivisaar, M., Kapley, A., Santos, P.M., 2019. Seasonal bacterial community dynamics in a crude oil refinery wastewater treatment plant. Applied Microbiology and Biotechnology 103, 9131-9141.

https://doi.org/10.1007/s00253-019-10130-8

The biological treatment of oil refinery effluents in wastewater treatment plants (WWTPs) relies on specialized bacteria contributing to remove organic load, nitrogen, sulfur, and phosphorus compounds. Knowledge about bacterial dynamics in WWTPs and how they affect the performance of the wastewater treatment is limited, particularly in tropical countries. The bacterial communities from three compartments of an oil refinery WWTP in Uran, India, were assessed using 16S-metabarcoding, in winter and monsoon seasons, upstream (from the surge pond) and downstream the biotower (clarifier and guard pond), to understand the effects of seasonal variations in WWTP’s efficiency. The organic load and ammonia levels of the treated wastewater increased by 3- and 9-fold in the monsoon time-point. A decreased abundance and diversity of 47 genera (325 OTUs) comprising ammonia and nitrite oxidizing bacteria (AOB, NOB, denitrifiers) was observed in the monsoon season downstream the biotower, whereas 23 OTUs of Sulfurospirillum, Desulfovibrio, and Bacillus, putatively performing dissimilatory nitrate reduction to ammonia (DNRA), were 3-fold more abundant in the same compartments (DNRA/denitrifiers winter ratio < 0.5 vs. monsoon ratio around 3). The total abundance of reported sulfate- and sulfite-reducing bacteria also increased 250- and 500-fold downstream the biotower, in the monsoon time-point. Bacteria performing DNRA may thus outcompete denitrification in this WWTP, limiting the biodegradation process. The alterations detected in bacterial populations involved in the removal of nitrogen and sulfur species evidenced a

reduced quality of the released wastewater and may be good candidates for the following monitoring strategies and optimization of the wastewater treatment.


https://doi.org/10.1007/s00216-019-02108-2

In this work, laser desorption ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (LDI–FTICRMS) was used to investigate the molecular composition of a peat fire and laboratory heated soil organic matter (SOM). SOM isolated from soils obtained from unburned and burned sites at Central Kalimantan, Indonesia, were analyzed with LDI–FTICRMS. About 7500 peaks were found and assigned with molecular formulas for each mass spectrum. SOM isolated from fire-affected soil sites are relatively more abundant in low oxygenated classes (e.g., O1–O5) and thermally stable compounds, including condensed hydrocarbon and nitrogen heterocyclic compounds. Abundances of highly condensed hydrocarbon compounds with carbon number > 30 were increased for the fire-affected SOM. In vivo heating experiments were conducted for SOM extracted from unburned sites, and the prepared SOMs were analyzed with LDI–FTICRMS. Overall, the same trend of change at the molecular level was observed from both the laboratory heated and the peat fire-affected SOM samples. In addition, it was observed that heat caused the degradation of SOM, generating lignin and tannin-type molecules. It was hypothesized that they were formed by thermal degradation of high molecular weight SOM. All the information presented in this study was obtained by consuming ~ 5 μg of sample. Therefore, this study shows that LDI–FTICRMS is a sensitive analytical technique that is effective in obtaining molecular level information of SOM.

Soltani, P., Sadeghnejad, S., Saeedi Dehaghani, A.H., Ashena, R., 2019. Quantitative monitoring of cleaning time and wettability alteration of carbonate rocks during soxhlet cleaning. SPE Reservoir Evaluation & Engineering 22, 1334-1345.

https://doi.org/10.2118/197066-PA

Core analysis is one of the most important steps in formation evaluation. The availability of routine-core-analysis (RCAL) and special-core-analysis (SCAL) data results in a better characterization of reservoirs and prediction of their behaviors. Unfortunately, the process of running core experiments, in both RCAL and SCAL phases, is very time consuming. Because all plug samples should be cleaned during the RCAL phase, finding a solvent that can speed up this process is desirable. The cleanliness of a core sample during Soxhlet extraction is usually determined by monitoring the color of solvents qualitatively. The main contribution of this study is to propose a methodology during RCAL to determine the best solvent during the Soxhlet-cleaning experiments. By introducing a novel quantitative method, the cleaning time of different solvents (i.e., tetrachloroethene, acetone, toluene, chloroform, xylene, and n-hexane) is investigated. This quantitative method is based on turbidity measurement of the solvent that siphons periodically from the Soxhlet extractor. Moreover, the wettability alteration of the implemented solvents is monitored by contact-angle measurements. To perform the analysis, two crude-oil samples (a heavy oil and a light oil with different asphaltene/resin fractions) and carbonate rocks from two Iranian formations are implemented. The results show that the polar solvents can speed up the cleaning

process while altering the wettability of the carbonate samples toward more-water-wet conditions. The introduced methodology of measuring the cleaning time can be implemented as a routine screening tool in RCAL projects to determine the proper solvent that can reduce the Soxhlet-cleaning time.

Song, N., Bai, L., Xu, H., Jiang, H.-L., 2020. The composition difference of macrophyte litter-derived dissolved organic matter by photodegradation and biodegradation: Role of reactive oxygen species on refractory component. Chemosphere 242, 125155.


The overgrowth of macrophytes has become serious due to increasing eutrophication in shallow lakes. The primary degradation processes of macrophytes litter, including photodegradation and biodegradation, induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM). In this study we investigated the composition evolution of DOM derived from emergent aquatic plant litter, Phragmites australis, in microbial degradation, photodegradation, and the combination of bio- and photo-degradation. Results revealed that the effects of photo- and biodegradation on the composition difference of macrophyte litter-derived DOM during short- and long-term degradation phase were different. Although large changes in DOM were observed after five days of incubation, the abundance and chemical composition were similar in the three treatments. However, more concentration of DOM was produced by combined photo- and biodegradation at the long-term degradation phase, and the composition of DOM showed less lignin-like formulae, as well as less condensed aromatic and aromatic compounds when compared to sole treatments. More reactive oxygen species (ROS) were found under the combined treatments, thus the contents of refractory components (condensed aromatic- and aromatic compound groups) were reduced. This study provide deeper insight into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.

Song, Y., Hu, S., Xu, J., Shen, C., Li, S., Su, P., Xie, W., 2020. Lacustrine environmental evolution and implications on source rock deposition in the Upper Cretaceous-Paleocene of the South Yellow Sea Basin, offshore eastern China. Marine and Petroleum Geology 113, 104135.


Lacustrine source rocks are well developed within the Upper Cretaceous-Paleocene in the South Yellow Sea Basin (SYSB) in offshore eastern China. Understanding the deposition of these source rocks could provide critical information for hydrocarbon exploration in the SYSB, as well as reveal the paleoenvironment across the Cretaceous/Paleogene boundary in eastern China. This study investigates the lacustrine environmental evolution during the Upper Cretaceous Taizhou Formation (K2t) to Paleocene Funing Formation (E1f) within the SYSB and its implications on source rock deposition based on core observation combined with organic geochemical indicators. Multiple maturity parameters (vitrinite reflectance, Tmax and biomarker isomerization ratios) reveal that the organic matter (OM) has reached early oil window maturity. The OM of source rocks is dominated by kerogen Type II-III (liptinite and vitrinite). Anoxic, saline-brackish deep to semi-deep lacustrine environments prevailed during the deposition of K2t2 (second member of the K2t), E1f2 (second member of the E1f) and E1f4L (lower unit of fourth member of the E1f). The deposition of three intervals was influenced by marine incursion, as evidenced by geochemical and paleontological

results. Low to moderate TOC contents (avg. 0.78 wt% to 1.91 wt%), which corresponds to low to moderate terrestrial OM input, are observed through three intervals. Abundant freshwater, together with high terrestrial OM flowed into the lacustrine environments during the deposition of E1f4U (upper unit of fourth member of the E1f), leading to dysoxic-oxic and freshwater conditions. High terrestrial OM input is probably the major controlling factor for relatively high TOC contents (avg. 2.49%) in the E1f4U. An evolution from balanced-fill to overfilled lake-type is observed in the Upper Cretaceous-Paleocene of SYSB, consistent with an evolution from semi-arid to humid paleoclimate conditions. The E1f4U and E1f2 source rocks exhibit fair to good potential, whereas poor to fair potential is present in the E1f4L and K2t2 source rocks. Compared with the Paleogene source rocks in onshore eastern China, the Upper Cretaceous-Paleocene source rocks in the SYSB probably hold good potential for generating commercial quantity of oil, although further study on hydrocarbon generation kinetics of source rocks and overall basin history are needed.

Song, Y., Wang, X., Guo, X., Liu, C., Li, H., Liu, D., 2020. Analysis on causes of differences in physical properties of Jurassic crude oil around Fukang depression, Junggar Basin. Petroleum Science and Technology 38, 75-82.

https://doi.org/10.1080/10916466.2019.1664571

According to the differences in physical properties of Jurassic crude oil around Fukang depression, geochemical characteristics of oil are analyzed from five zones. The results show that differences in organic matter and biodegradation are the causes of differences in physical properties. Crude oil in Ganhe and Santai oilfield come from Permian sapropel source rocks. Because of biodegradation, crude oil in Santai oilfield was heavier. Due to multistage charging and biodegradation, crude oil in Fudong slope is characterized by mixed with normal density. The light oil in Fubei slope and Fukang depression belong to the products of Jurassic humic source rocks.

Soudzilovskaia, N.A., van Bodegom, P.M., Terrer, C., Zelfde, M.v.t., McCallum, I., Luke McCormack, M., Fisher, J.B., Brundrett, M.C., de Sá, N.C., Tedersoo, L., 2019. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nature Communications 10, 5077.

https://doi.org/10.1038/s41467-019-13019-2

Vegetation impacts on ecosystem functioning are mediated by mycorrhizas, plant–fungal associations formed by most plant species. Ecosystems dominated by distinct mycorrhizal types differ strongly in their biogeochemistry. Quantitative analyses of mycorrhizal impacts on ecosystem functioning are hindered by the scarcity of information on mycorrhizal distributions. Here we present global, high-resolution maps of vegetation biomass distribution by dominant mycorrhizal associations. Arbuscular, ectomycorrhizal, and ericoid mycorrhizal vegetation store, respectively, 241 ± 15, 100 ± 17, and 7 ± 1.8 GT carbon in aboveground biomass, whereas non-mycorrhizal vegetation stores 29 ± 5.5 GT carbon. Soil carbon stocks in both topsoil and subsoil are positively related to the community-level biomass fraction of ectomycorrhizal plants, though the strength of this relationship varies across biomes. We show that human-induced transformations of Earth’s ecosystems have reduced ectomycorrhizal vegetation, with potential ramifications to terrestrial carbon stocks. Our work provides a benchmark for spatially explicit and globally quantitative assessments of mycorrhizal impacts on ecosystem functioning and biogeochemical cycling.

Spatharis, S., Lamprinou, V., Meziti, A., Kormas, K.A., Danielidis, D.D., Smeti, E., Roelke, D.L., Mancy, R., Tsirtsis, G., 2019. Everything is not everywhere: can marine compartments shape phytoplankton assemblages? Proceedings of the Royal Society B: Biological Sciences 286, 20191890.


The idea that ‘everything is everywhere, but the environment selects' has been seminal in microbial biogeography, and marine phytoplankton is one of the prototypical groups used to illustrate this. The typical argument has been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative roles of compartmentalization of regional seas and site-specific environmental conditions in shaping assemblage structures have not been specifically examined. We collected data from coastal embayments that fall within two different water compartments within the same regional sea and are characterized by highly localized environmental pressures. We used principal coordinates of neighbour matrices (PCNM) and asymmetric eigenvector maps (AEM) models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our models explained a high percentage of variation in assemblage composition (59–65%) and showed that spatial structure consistent with marine compartmentalization played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalization. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere.

Spraggins, J.M., Djambazova, K.V., Rivera, E.S., Migas, L.G., Neumann, E.K., Fuetterer, A., Suetering, J., Goedecke, N., Ly, A., Van de Plas, R., Caprioli, R.M., 2019. High-performance molecular imaging with MALDI trapped ion-mobility time-of-flight (timsTOF) mass spectrometry. Analytical Chemistry 91, 14552-14560.


Imaging mass spectrometry (IMS) enables the spatially targeted molecular assessment of biological tissues at cellular resolutions. New developments and technologies are essential for uncovering the molecular drivers of native physiological function and disease. Instrumentation must maximize spatial resolution, throughput, sensitivity, and specificity, because tissue imaging experiments consist of thousands to millions of pixels. Here, we report the development and application of a matrix-assisted laser desorption/ionization (MALDI) trapped ion-mobility spectrometry (TIMS) imaging platform. This prototype MALDI timsTOF instrument is capable of 10 μm spatial resolutions and 20 pixels/s throughput molecular imaging. The MALDI source utilizes a Bruker SmartBeam 3-D laser system that can generate a square burn pattern of <10 × 10 μm at the sample surface. General image performance was assessed using murine kidney and brain tissues and demonstrate that high-spatial-resolution imaging data can be generated rapidly with mass measurement errors <5 ppm and ∼40 000 resolving power. Initial TIMS-based imaging experiments were performed on whole-body mouse pup tissue demonstrating the separation of closely isobaric [PC(32:0) + Na]+ and [PC(34:3) + H]+ (3 mDa mass difference) in the gas phase. We have shown that the MALDI timsTOF platform can maintain reasonable data acquisition rates (>2 pixels/s) while providing the specificity necessary to differentiate components in complex mixtures of lipid adducts. The combination of high-spatial-resolution and throughput imaging capabilities with high-performance TIMS separations provides a

uniquely tunable platform to address many challenges associated with advanced molecular imaging applications.

Stevens, J.C., Shi, J., 2019. Biocatalysis in ionic liquids for lignin valorization: Opportunities and recent developments. Biotechnology Advances 37, 107418.


Lignin holds tremendous potential as a renewable feedstock for upgrading to a number of high-value chemicals and products that are derived from the petroleum industry at present. Since lignin makes up a significant fraction of lignocellulosic biomass, co-utilization of lignin in addition to cellulose and hemicelluloses is vital to the economic viability of cellulosic biorefineries. The recalcitrant nature of lignin, originated from the molecule's compositional and structural heterogeneity, however, poses great challenges toward effective and selective lignin depolymerization and valorization. Ionic liquid (IL) is a powerful solvent that has demonstrated high efficiency in fractionating lignocellulosic biomass into sugar streams and a lignin stream of reduced molecular weight. Compared to thermochemical methods, biological lignin deconstruction takes place at mild temperature and pressure while product selectivity can be potentially improved via the specificity of biocatalysts (lignin degrading enzymes, LDEs). This review focuses on a lignin valorization strategy by harnessing the biomass fractionating capabilities of ILs and the substrate and product selectivity of LDEs. Recent advances in elucidating enzyme-IL interactions as well as strategies for improving enzyme activity in IL are discussed, with specific emphases on biocompatible ILs, thermostable and IL-tolerant enzymes, enzyme immobilization, and surface charge engineering. Also reviewed is the protein engineering toolsets (directed evolution and rational design) to improve the biocatalysts' activity, stability and product selectivity in IL systems. The alliance between IL and LDEs offers a great opportunity for developing a biocatalytic route for lignin valorization.

Stoll, D.R., Lhotka, H.R., Harmes, D.C., Madigan, B., Hsiao, J.J., Staples, G.O., 2019. High resolution two-dimensional liquid chromatography coupled with mass spectrometry for robust and sensitive characterization of therapeutic antibodies at the peptide level. Journal of Chromatography B 1134-1135, 121832.


Separations of complex peptide mixtures have been a common target application for two-dimensional liquid chromatography over the last few decades. These separations have most frequently been carried out at the capillary scale, with columns on the order of 75 µm i.d. and flow rates on the order of 500 nL/min. Recently, however, several groups have worked to optimize comprehensive 2D-LC (LC × LC) separations of peptides at the analytical scale (i.e., 2 mm i.d. columns, and ca. 1 mL/min flow rates) and demonstrated peak capacities on the order of 5000 in analysis times of a few hours, using reversed-phase separations in both dimensions. In this paper we aim to advance the performance of such separations in two primary ways. First, we demonstrate that active solvent modulation (ASM) can be used to improve the 2D peak capacity by both enabling use of long and highly efficient first dimension (1D) columns, and by mitigating the deleterious effects of injecting large fractions of 1D effluent into the small columns that are required for fast and highly sensitive second dimension (2D) separations. Taken together these two benefits enable the

realization of a peak capacity of 10,000 in an analysis time of four hours. This comes at the cost of increased instrument complexity compared to 1D-LC separations, but the 2D-LC approach is unquestionably the most efficient way to improve upon the resolving power of existing 1D-LC. Second, we have systematically studied the compromise between the peak capacity of each 2D separation and the operating pressure required to achieve that peak capacity. Understanding this compromise will be important to the development of LC × LC methods that both produce high peak capacities, and are sufficiently robust to operate for days at a time without significant losses in separation performance. Based on the results of this study we chose conditions for subsequent separations that required less than 400 bar operating pressure in the second dimension, but yielded a 2D peak capacity of about 3500 in 2 h. After 160 h of continuous operation of the LC × LC separation under these conditions (and about 20,000 injections into the 2D column) the 2D column had only lost about 18% of its initial isocratic efficiency. These results should motivate further development and implementation of such high performing and robust separations for the identification and quantification of peptides in a variety of application areas, including digests of therapeutic proteins such as monoclonal antibodies.

Stovbun, S.V., Zanin, A.M., Shashkov, M.V., Skoblin, A.A., Zlenko, D.V., Tverdislov, V.A., Mikhaleva, M.G., Taran, O.P., Parmon, V.N., 2019. Spontaneous resolution and super-coiling in xerogels of the products of photo-induced formose reaction. Origins of Life and Evolution of Biospheres 49, 187-196.

https://doi.org/10.1007/s11084-019-09583-8

This work addresses the supramolecular self-organization in the xerogels of formose reaction products. The UV-induced formose reaction was held in over-saturated formaldehyde solutions at 70∘C without a catalyst. The solutions of the obtained carbohydrates were dried on a glass slide, and the obtained xerogels demonstrated a prominent optical activity, while the initial solutions were optically inactive. The xerogels contained highly elongated crystalline elements of a helical structure as well as the isometric ones. Thus xerogel formation was accompanied by a spontaneous resolution of enantiomers and separation of different-shaped supramolecular structures. The thick helices were twisted of thinner ones, while the latter were twisted of elementary structures having a diameter much smaller than 400 nm. Similar structural hierarchy is typical of biological macromolecules (DNA, proteins, and cellulose). Summarizing the obtained results, we proposed a hypothetical mechanism explaining the amplification of the initial enantiomeric excess, as well as chiral and chemical purification of the substances which were essential for the evolution of Life to start.

Stoyanovich, S.S., Yang, Z., Hanson, M., Hollebone, B.P., Orihel, D.M., Palace, V., Rodriguez-Gil, J.L., Faragher, R., Mirnaghi, F.S., Shah, K., Blais, J.M., 2019. Simulating a spill of diluted bitumen: Environmental weathering and submergence in a model freshwater system. Environmental Toxicology and Chemistry 38, 2621-2628.


The main petroleum product transported through pipelines in Canada is diluted bitumen (dilbit), a semiliquid form of heavy crude oil mixed with natural gas condensates to facilitate transport. The weathering, fate, behavior, and environmental effects of dilbit are crucial to consider when

responding to a spill; however, few environmental studies on dilbit have been completed. We report on 11 d long experimental spills of dilbit (Cold Lake Winter Blend) in outdoor microcosms meant to ‐ ‐simulate a low energy aquatic system containing natural lake water and sediments treated with low ‐(1:8000 oil:water) and high (1:800 oil:water) volumes of dilbit. In the first 24 h of the experiment, volatile hydrocarbons quickly evaporated from the dilbit, resulting in increased dilbit density and viscosity. These changes in dilbit's physical and chemical properties ultimately led to its submergence after 8 d. We also detected rapid accumulation of polycyclic aromatic compounds in the water column of the treated microcosms following the spills. The present study provides new information on the environmental fate and behavior of dilbit in a freshwater environment that will be critical to environmental risk assessments of proposed pipeline projects. In particular, the study demonstrates the propensity for dilbit to sink under ambient environmental conditions in freshwaters typical of many boreal lakes.

Stricker, C.A., Drexler, J.Z., Thorn, K.A., Duberstein, J.A., Rossman, S., 2019. Carbon chemistry of intact versus chronically drained peatlands in the southeastern USA. Journal of Geophysical Research: Biogeosciences 124, 2751-2767.

https://doi.org/10.1029/2019JG005079

Abstract The Great Dismal Swamp National Wildlife Refuge (GDS) is a large temperate swamp in Virginia/North Carolina, USA with peat soils historically resistant to microbial decomposition. However, this peatland has been subject to ~200 years of disturbance during which extensive drainage, fire suppression, and widespread logging have increased decomposition and dramatically decreased the distribution of Atlantic white cedar (AWC). The purpose of this study was to determine the impact of long-term drainage and AWC loss on the carbon chemistry of GDS peats. Peat cores were collected from three drained GDS vegetation communities (pocosin, AWC, and red maple-black gum) and compared to cores collected from an intact, undrained AWC peatland at the Alligator River National Wildlife Refuge (AR) in North Carolina. The AR peats had higher lignin content in the deeper peat intervals, and lignin content and percent organic carbon were largely invariant with depth compared to the GDS peats. The concentrations of syringyl group phenols were greater in the surface layers of GDS peats, likely reflecting the selective removal of AWC and transition from gymnosperms to angiosperms. Acid to aldehyde ratios for vanillyl and syringyl group phenols indicated that the GDS peats were more decomposed, particularly at depth, and that this occurred under aerobic conditions. Moreover, solid-state 13C NMR confirmed a coincident loss of carbohydrates and increase in recalcitrant by-products of carbohydrate degradation with depth. These data indicate that long-term drainage has accelerated the decomposition of peat at the GDS, reducing the capacity and stability of the carbon sink.

Struch, R.E., Pulster, E.L., Schreier, A.D., Murawski, S.A., 2019. Hepatobiliary analyses suggest chronic PAH exposure in hakes (Urophycis spp.) following the Deepwater Horizon oil spill. Environmental Toxicology and Chemistry 38, 2740-2749.


Prior to the Deepwater Horizon oil spill, we lacked a comprehensive baseline of oil contamination in the Gulf of Mexico's sediments, water column, and biota. Gaps in prespill knowledge limit our ability to determine the aftereffects of the Deepwater Horizon blowout or prepare to mitigate similar

impacts during future oil spill disasters. We examined spatiotemporal differences in exposure to and metabolism of polycyclic aromatic hydrocarbons (PAHs) in 2 hake species (Urophycis spp.) to establish a current baseline for these ecologically important, abundant, and at risk demersal fishes. ‐Gulf hake (Urophycis cirrata) and southern hake (Urophycis floridana) were collected throughout the Gulf of Mexico during extensive longline surveys from 2012 to 2015. Analyses of biliary PAH metabolites and liver PAH concentrations provided evidence of exposures to di and tricyclic ‐compounds, with the highest concentrations measured in the northern Gulf of Mexico. Species‐specific differences were not detected, but temporal trends observed in biliary PAHs suggest a decrease in acute exposures, whereas increasing liver PAHs suggest chronic exposures marked by greater assimilation than metabolism rates. To our knowledge, the present study provides the first multitissue contaminant analyses, as well as the most exhaustive biometric analyses, for both gulf and southern hakes. Though sources of exposure are complex because of multiple natural and anthropogenic PAH inputs, these results will facilitate the development of much needed health metrics for Gulf of Mexico benthos.

Subirats, X., Abraham, M.H., Rosés, M., 2019. Characterization of hydrophilic interaction liquid chromatography retention by a linear free energy relationship. Comparison to reversed- and normal-phase retentions. Analytica Chimica Acta 1092, 132-143.


The Abraham solvation parameter model, a linear free energy relationship (LFER) approach, has been used to characterize a polymeric zwitterionic (sulfobetaine) column in HILIC mode. When acetonitrile (MeCN) is used in the preparation of mobile phases the main solute characteristics affecting the chromatographic behavior of analytes are the molecular size and the hydrogen-bonding (both acidity and basicity) interactions. The former property is more favorable in the acetonitrile-rich mobile phase, reducing thus the retention, but the latter reveals a higher affinity for the water layer adsorbed on the stationary phase, enhancing retention. However, if the aprotic acetonitrile is replaced by methanol, a hydrogen-bond acidic solvent, solute hydrogen-bond basicity does not contribute any more to retention, quite the opposite. Thus, a slightly different selectivity is observed in methanol/water than in acetonitrile/water. Normal-phase mode and HILIC-MeCN share the same main factors affecting retention. For reversed-phase and immobilized artificial membrane (IAM) chromatography, the solute molecular size increase retention because of the lower amount of energy required in the formation of a cavity in the solvated stationary phase. On the contrary, the analyte hydrogen-bond basicity favors interactions with the hydroorganic mobile phase and reduces retention. The determined parameters justify the reversed selectivity commonly observed in HILIC in reference to reversed-phase. In most instances, the least retained solutes in reversed-phase are the most retained in HILIC.

Sun, H., Chen, B., Yang, M., 2020. Effect of multiphase flow on natural gas hydrate production in marine sediment. Journal of Natural Gas Science and Engineering 73, 103066.


Natural gas hydrates (NGHs), regarded as an alternative future energy source. Currently, tests for hydrate exploitation from marine sediment have been performed in the Nankai Trough of Japan and the Shenhu area of the South China Sea. Hydrate exploitation is influenced by water-gas flow in the

sediment, and considering the huge seawater reserves in hydrate accumulation areas, an experiment of seawater-gas flow was performed to dissociate hydrate. The effects of seawater-gas flow rates and initial hydrate saturation on methane hydrate (MH) production were analyzed. The results showed that seawater-gas flow efficiently promotes hydrate dissociation and inhibits hydrate reformation. Moreover, there was a faster heat and mass transfer with increasing seawater flow rates and decreasing gas flow rates, which enhanced the average MH dissociation rate. In addition, the variation time of the flow channel increased with higher initial hydrate saturation. Additionally, seawater-gas flow promotes MH dissociation stronger than deionized water-gas flow.



Peat properties including porosity, dry bulk density (DBD), ash content (and their XRD and SEM), TOC, humification and plant macrofossil were measured in the well dated, young peat profiles of Jinchuan Mire in southeast Jilin of China. Base on the properties and depositional rates (Li et al., 2019) of JC1 (50-cm long) and JCA (92-cm long), carbon accumulation rates (RCAs) have been calculated for different periods and processes of peatland development over the past 1000 years have been described. The long term variations of the RCAs between Jinchuan Mire and nearby Baijianghe Mire (Xia et al., 2019) during the past 1000 years matched reasonably well, reflecting similar carbon accumulation rates under the same climatic control even though the plant species could be very different in the two mires. Enhanced detrital content caused by surface runoff due to heavy rains with decline of wood% in plant remains probably reflect wet climates; and vice versa. In comparisons with regional climatic records, we describe the development of Jinchuan Mire as follow: (1) relatively warm and wet climates between 1000 CE and 1150 CE reflected by dominant herb species (>95%) with low wood% and no Sphagnum%, low DBD and detritus, and high TOC% and porosity. A dry climate occurred during 1150–1200 CE to lower the water table and enable growth of mosses in the mire. (2) Wet and cooling conditions during 1200–1370 CE supported well development of Sphagnum mosses and good development of the mire. (3) A climatic change from wet/cool to cold/dry between 1370 CE and 1440 CE caused disappear of Sphagnum mosses. (4) During the Little Ice Age (1440–1850 CE), cold and dry conditions led to poor peat development without Sphagnum mosses. (5) After 1850 CE, warm and wet conditions were in favor of aquatic herb growth. (6) Human impact caused anomaly peat accumulation with mainly tree species and detritus between 1950 and 1965. The peatland has been recovered from natural condition and development of Sphagnum mosses since 1965. Estimated RCAs in the hummock site and the lawn site are 320 gC/m2/y and 63 gC/m2/y, respectively during 1970–2010. Estimation of carbon accumulation over the entire peatland needs more work.

Sun, L., Yin, C., Liu, C., Zeng, H., Zhang, Y., Xu, Y., Cai, D., 2019. Geological characteristics and exploration significance of high-quality source rocks in Yingcheng Formation, Songliao Basin. Acta Petrolei Sinica 40, 1172-1179.


In order to comprehensively and effectively recognize source rocks in Yingcheng Formation of Shuangcheng area in Songliao Basin, the geochemical pyrolysis and molecular organic geochemistry characteristics of drilled core are analyzed, high-abundance mature source rocks have been found for the first time. Combining sequence stratigraphy and geophysical techniques, the distribution law of high-quality source rocks is determined. It was recognized that the average total organic carbon (TOC)content is 2.46%, the organic matter is mainly Ⅱ type, there are a plenty of aquatic algae in organic matter, and the vitrinite reflectance (Ro)is in a range of 0.8% -1.0%, so the source rocks are in the peak hydrocarbon-generating stage. A relatively stable tectonic background of fault depression conversion period is a favorable environment for source rocks deposition, low Pr/Ph ratio of nalkane proved favorable environment for the preservation of organic matter. The high-quality source rocks mainly developed in the transgressive system tract and highstand system tract of sequence SQ1 and sequence SQ2, the thickness of high-quality source rocks in SQ1 is generally 20-80 m, while the thickness of high-quality source rocks in SQ2 is generally 10-30 m. The oil source correlation shows that the high-quality source rocks in Shuangcheng area are the direct hydrocarbon source for the reservoir, and the discovery of high-quality source rocks in Shuangcheng area provides reference for other peripheral fault depression exploration.



An evaluation of shale pore connectivity is essential for predicting the production behavior and optimizing the development plan of shale gas. To systematically investigate the multiscale connectivity characteristics and controlling factors, complementary tests were conducted on four overmature marine shale samples from southern China (one each from Longmaxi Formation and Wufeng Formation, and two from Niutitang Formation) with different maturity and composition. The methods included mercury intrusion capillary pressure (MICP), spontaneous imbibition with deionized water and n-decane, saturated diffusion distribution with seven nano-sized tracers, N2 physisorption, small-angle neutron scattering (SANS), and focused ion beam-scanning electron microscopy (FIB-SEM) tomography. Moreover, a novel repeated MICP measurement technique was developed and used to evaluate the pore connectivity from the distribution behavior of residual mercury. Results indicate that the connectivity loss of hydrophilic pore networks owing to an increased maturity and the compaction causes pore shrinkage and bond breakage between pore networks. According to the three-dimensional reconstruction and pore network extraction of FIB-SEM images, pores in organic matter (OM) have a good pore connectivity, but the minerals surrounding the OM reduce the overall pore connectivity of the shale matrix. By evaluating the pore connectivity using different methods, the hydrocarbon migration pattern in overmature marine shales was established. Our results imply that in addition to creating induced fracture networks, effectively connecting induced fractures with preexisting microcracks or joint sets between OM pore networks and transport pores can also be used to enhance overall pore connectivity. Microwave heating in shale reservoirs may be an effective way of further improving the production and recovery of hydrocarbons.

Sun, W.-C., Yin, Z.-J., Donoghue, P., Liu, P.-J., Shang, X.-D., Zhu, M.-Y., 2019. Tubular microfossils from the Ediacaran Weng’an Biota (Doushantuo Formation, South China) are not early animals. Palaeoworld 28, 469-477.


The early Ediacaran Weng’an Biota (ca. 609 Ma) of the Doushantuo Formation (Guizhou Province, China) encompasses an abundant and exquisitely preserved assemblage of phosphatic microfossils that have provided unique insight into the origin and early evolution of multicellular eukaryotes. However, the affinities of these early organisms are far from certain, including the tubular microfossils Crassitubulus, Quadratitubus, Ramitubulus, and Sinocyclocylcicus. These taxa have been widely accepted as stem-cnidarians or, alternatively, interpreted as filamentous cyanobacteria, or multicellular algae. We use high-resolution X-ray tomographic microscopy to analyse the structure and development of the four taxa. Our data and analysis allow us to conclude that these four taxa were not biomineralized. Crassitubulus, Quadratitubus, and Sinocyclocylcicus, may be grouped on the basis that they exhibit alternating complete and incomplete cross walls, and bipolar growth; which makes them favourably comparable to filamentous cyanobacteria. In contrast, Ramitubulus exhibits only complete cross walls, unipolar growth and dichotomous branching. These features are difficult to reconcile with a cyanobacterial interpretation. They are, instead, more indicative of multicellular algae-like Cambrian Epiphyton. Thus, the Weng’an tubular microfossils constitute a disparate assemblage of cyanobacteria and algae, but none represents early Ediacaran animals.


https://doi.org/10.1155/2019/5047643

Hydraulic fracturing is widely applied to economic gas production from shale reservoirs, but the effect of the shale mineral composition on the physical-chemical reactions during hydraulic fracturing is still poorly understood. To develop a foundational understanding of chemical interactions occurring on shale with different mineralogical compositions, two different types of mineral composition marine shale (carbonate-poor and carbonate-rich) from the Niutitang Formation were reacted with slick water fracturing fluid in a laboratory reactor at 100°C and 50 MPa for three days. To identify the changes of the pore structure characteristics during hydraulic fracturing, the field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), low-temperature nitrogen adsorption, and porosity measurement were performed on the original and treated shale samples. After the slick water treatment, the dissolution of pyrite in carbonate-poor shale (obtained from Youyang County, labeled as YY) was observed by FE-SEM and XRD analyses, while in carbonate-rich shale (obtained from Guzhang County, labeled as GZ), the carbonate dissolution was observed. Results from the low-temperature N2 adsorption and porosity measurement demonstrated that the variation trend of pore structure characteristics for the YY and GZ shale samples was quite different after reacting with slick water fracturing fluid. For YY shale, the specific surface area, total pore volume, and porosity increased after the reaction, whereas an opposite trend was observed in the GZ shale. Moreover, the fractal dimension analysis illustrated that the pore surface became less rough and the pore structure became more complex in the YY shale, whereas the degree of pore surface roughness and pore structure complexity of the GZ shale was reduced. The results demonstrated that the initial mineralogical composition of shale played an important role in pore structure alteration during hydraulic fracturing.

Swindles, G.T., Morris, P.J., Mullan, D.J., Payne, R.J., Roland, T.P., Amesbury, M.J., Lamentowicz, M., Turner, T.E., Gallego-Sala, A., Sim, T., Barr, I.D., Blaauw, M., Blundell, A., Chambers, F.M., Charman, D.J., Feurdean, A., Galloway, J.M., Gałka, M., Green, S.M., Kajukało, K., Karofeld, E., Korhola, A., Lamentowicz, Ł., Langdon, P., Marcisz, K., Mauquoy, D., Mazei, Y.A., McKeown, M.M., Mitchell, E.A.D., Novenko, E., Plunkett, G., Roe, H.M., Schoning, K., Sillasoo, Ü., Tsyganov, A.N., van der Linden, M., Väliranta, M., Warner, B., 2019. Widespread drying of European peatlands in recent centuries. Nature Geoscience 12, 922-928.

https://doi.org/10.1038/s41561-019-0462-z

Climate warming and human impacts are thought to be causing peatlands to dry, potentially converting them from sinks to sources of carbon. However, it is unclear whether the hydrological status of peatlands has moved beyond their natural envelope. Here we show that European peatlands have undergone substantial, widespread drying during the last ~300 years. We analyse testate amoeba-derived hydrological reconstructions from 31 peatlands across Britain, Ireland, Scandinavia and Continental Europe to examine changes in peatland surface wetness during the last 2,000 years. We find that 60% of our study sites were drier during the period 1800–2000 ce than they have been for the last 600 years, 40% of sites were drier than they have been for 1,000 years and 24% of sites were drier than they have been for 2,000 years. This marked recent transition in the hydrology of European peatlands is concurrent with compound pressures including climatic drying, warming and direct human impacts on peatlands, although these factors vary among regions and individual sites. Our results suggest that the wetness of many European peatlands may now be moving away from natural baselines. Our findings highlight the need for effective management and restoration of European peatlands.



Chemical evolution is an abiotic reaction process in which complex organic molecules arise from a combination of simple inorganic and organic chemical compounds. To assess the possible ongoing chemical evolution in the subsurface ocean of Saturn’s icy satellite Enceladus, we explored the water–rock aqueous reactions and the peptide formation capability under a hydrothermal environment similar to that on Enceladus. It has been suggested that the core of Enceladus has not experienced high temperatures from the time of satellite formation to the present. The major components of the core are assumed to be carbonaceous chondrites; thus, simple organic substances, including amino acids, are likely present in the alkaline seawater of Enceladus. In this study, we conducted a laboratory-based simulation experiment to describe the chemical alteration of six prebiotically abundant amino acids over 147 days under high pressure with thermal cycling (30 to 100 °C) to simulate the water–rock interface of the ocean on Enceladus. As a result, we detected 28 out of 36 possible dipeptide species during the entire reaction period. We propose that peptide-bond formation is coupled to rock surface chemisorption of amino acids under alkaline condition, which was further supported by the elemental analysis showing carbon and nitrogen signature on the rock surface only when amino acids are added. The above result suggests that ongoing chemical evolution on Enceladus is likely producing short abiotic peptides on the porous core surface.



Abstract: A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus

Methanoregula (order Methanomicrobiales); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria, which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, “Candidatus Hydrogenosomobacter endosymbioticus.”

Importance: Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates.

Takis, P.G., Ghini, V., Tenori, L., Turano, P., Luchinat, C., 2019. Uniqueness of the NMR approach to metabolomics. TrAC Trends in Analytical Chemistry 120, 115300.


NMR measures a relatively small portion of the human metabolome, which roughly corresponds to all free small molecules present in concentrations ≥1 μM. However, the method is intrinsically quantitative and highly reproducible and, whenever standardized pre-analytical and analytical procedures are used, it allows for fast fingerprinting and profiling of a variety of biosamples. While developing methods for accurate and automated identification and quantitation of detectable metabolites, we have proposed a Urine Shift Predictor that also provides the concentration of NMR-invisible inorganic ions. For biomedical applications, two peculiar features are associated to the fast, untargeted NMR-metabolomic fingerprinting of biofluids, i.e. the ability to: i) identify the individual phenotype that constitutes the metabolic signature of a person and monitor its behavior over time; ii) identify the signature of different diseases. The combination of the two in longitudinal cohort studies could become a tool for fast and untargeted screening of populations.

Tan, S.P., Kargel, J.S., Vance, S.D., Lopes, R.M., 2019. Modeling binary mixtures of water + light hydrocarbon using the perturbed-chain statistical associating fluid theory with induced association: Improvement in describing all equilibrium phases. ACS Earth and Space Chemistry 3, 2569-2581.


Hydrophobic effects, including low mutual solubilities, are well-documented between water and hydrocarbons. However, as deduced from quantum chemical calculations and molecular simulations, an attractive interaction as a result of electrostatic interactions and induction by water on hydrocarbon molecules exists and must be included to adequately model water–hydrocarbon systems. As shown in this work, the inclusion of these interactions allows for the perturbed-chain statistical associating fluid theory equation of state (EOS) to perform well in all equilibrium phases. Without these corrections, the EOS usually performs well only for the phase used for parametrization. Because the EOS will also be used in near-freezing water temperatures, the parameters of water are carefully derived to be able to reproduce the density anomaly of water and behavior when extrapolated to the supercooled region. The improvements and calculations will be useful for the assessment of the occurrences of potentially habitable water-poor and water-rich environments within the ice crusts and rocky crusts of extraterrestrial bodies.



The improvement of microbial induced calcium carbonate precipitate (MICP) using additives has attracted much attention due to its great influence on the quality of precipitate. In this paper, graphene oxide (GO) was used as an additive to induce CaCO3 precipitate. Using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS), the effects of GO on immobilization of bacteria, CaCO3 crystals and the consolidation of sand was studied. The addition of GO caused the rapid growth and the larger size of the CaCO3

crystals. Additionally, the morphology of the rhombohedral crystals was unchanged. The precipitation capability of CaCO3 during the MICP process was improved significantly. X-ray diffraction (XRD) noted that stable calcite was formed during the CaCO3 precipitate process with GO, compared to calcite and vaterite formed. More importantly, the unconfined compressive strength of the consolidated sand was significantly enhanced. These results show that GO has outstanding properties.

Tang, X., Yu, P., Tang, L., Zhou, M., Fan, C., Lu, Y., Mathieu, J., Xiong, W., Alvarez, P.J., 2019. Bacteriophages from arsenic-resistant bacteria-transduced resistance genes, which changed arsenic speciation and increased soil toxicity. Environmental Science & Technology Letters 6, 675-680.

https://doi.org/10.1021/acs.estlett.9b00600

Lysogenic phages are known to serve as transfer vectors for bacterial genes involved in biotransformation of various environmental pollutants. However, their role in arsenic-contaminated environments is largely undocumented. Here, lysogenic phages were chemically induced (with mitomycin C) in soil samples from two contaminated sites, and arsenic resistance genes arsC (coding for As(V) reduction to excretable (via efflux pumps) but more toxic As(III)) and arsM (coding for As(III) methylation) were detected in these phage genomes. The relative abundance of these genes (per phage particle) was positively correlated with that in the corresponding indigenous soil bacterial communities (resistance gene per 16S rRNA), with R2 = 0.974 for arsC and 0.761 for arsM. Microcosm studies with 100 mg/kg of arsenic soil showed that phages (amended at 5.0 × 107 phages per gram soil) enhanced the propagation of arsC by 122-fold and arsM by 575-fold, relative to unamended soil. This increased the As(III) concentration by 4.3 mg/kg (214%) after 15 days but also enabled arsenic methylation (to 0.8 mg/kg). Earthworm avoidance tests corroborated the increase in soil arsenic ecotoxicity after phage addition. Overall, this study demonstrates that arsenic resistance genes transduction by lysogenic phages can result in an overlooked but important phenomenon: a change in arsenic speciation and a significant increase in soil ecotoxicity.

Tanikawa, W., Hirose, T., Hamada, Y., Gupta, L.P., Ahagon, N., Masaki, Y., Abe, N., Wu, H.Y., Sugihara, T., Nomura, S., Lin, W., Kinoshita, M., Yamamoto, Y., Yamada, Y., 2019. Porosity, permeability, and grain size of sediment cores from gas-hydrate-bearing sites and their implication for overpressure in shallow argillaceous formations: Results from the national gas hydrate program expedition 02, Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 332-347.


The existence of overpressure in shallow sediments, which is often constrained by hydraulic properties, influences the gas-hydrate formation process and gas production. Porosity, permeability, and grain size measurements in laboratory experiments were conducted on core samples from gas-hydrate-bearing regions offshore from the Krishna-Godavari Basin, eastern India. Porosity was found to decrease with increasing effective stress; this is explained by the exponential decay curve along which porosity decreases from 65 % at 0 MPa to 40 % at 10 MPa. Permeability and the corresponding hydraulic diffusivity decrease from 10−17 to less than 10−18 m2 and from 10−7 to 10−8 m2/s at 0.5 and 5 MPa, respectively. Grain sizes were larger and the sand fraction more scattered in channel-filled sediment sites compared to slope sediment sites. The preconsolidation stresses evaluated from consolidation curves indicate the absence of overpressure at shallow depths. In contrast, a comparison of ship-board measurements and standard compaction curves suggested that measured porosity was higher than the predicted porosity at greater depths. These porosity anomalies are interpreted as a sign of overpressure that approaches near lithostatic values at greater depths in slope sediment sites. A one-dimensional sedimentation model recreated overpressure profiles similar to those predicted by porosity gaps, under the

assumption of large basial fluid influx or lower permeability than that derived from laboratory data. The modeling results suggest that near-hydrostatic pressure at shallow depths and significant overpressure at greater depths proposed by the porosity gap method is explained by the non-linearity of transport properties. The relatively small overpressure generation in channel-filled sites compared with slope sites can be explained by the higher permeability due to coarser grain size and larger sand fraction and by the smaller basal influx. On the contrary, considerably large basal influx associated with clay mineral dehydration and methane gas supply from deep sediments was expected to promote overpressure at slope sites, which is confirmed by Cl− concentration-depth profiles.



Increased permafrost thaw due to climate change in northern high-latitudes has prompted concern over impacts on soil and stream biogeochemistry that affect the fate of dissolved organic carbon (DOC). Few studies to-date have examined the link between molecular composition and biolability of dissolved organic matter (DOM) mobilized from different soil horizons despite its importance in understanding carbon turnover in aquatic systems. Additionally, the effect of mixed DOM sources on microbial metabolism (e.g., priming) is not well understood. No studies to-date have addressed potential priming effects in northern high-latitude or permafrost-influenced aquatic ecosystems, yet these ecosystems may be hot spots of priming where biolabile, ancient permafrost DOC mixes with relatively stable, modern stream DOC. To assess biodegradability and priming of DOC in permafrost-influenced streams, we conducted 28 day bioincubation experiments utilizing a suite of stream samples and leachates of fresh vegetation and different soil horizons, including permafrost, from Interior Alaska. The molecular composition of unamended DOM samples at initial and final time points was determined by ultrahigh resolution mass spectrometry. Initial molecular composition was correlated to DOC biodegradability, particularly the contribution of energy-rich aliphatic compounds, and stream microbial communities utilized 50–56% of aliphatics in permafrost-derived DOM within 28 days. Biodegradability of DOC followed a continuum from relatively stable stream DOC to relatively biolabile DOC derived from permafrost, active layer organic soil, and vegetation leachates. Microbial utilization of DOC was ∼3–11% for stream bioincubations and ranged from 9% (active layer mineral soil-derived) to 66% (vegetation-derived) for leachate bioincubations. To investigate the presence or absence of a priming effect, bioincubation experiments included treatments amended with 1% relative carbon concentrations of simple, biolabile organic carbon substrates (i.e., primers). The amount of DOC consumed in primed treatments was not significantly different from the control in any of the bioincubation experiments after 28 days, making it apparent that the addition of biolabile permafrost-derived DOC to aquatic ecosystems will likely not enhance the biodegradation of relatively modern, stable DOC sources. Thus, future projections of carbon turnover in northern high-latitude region streams may not have to account for a priming effect.

Thompson-Butler, W., Peters, K.E., Magoon, L.B., Scheirer, A.H., Moldowan, J.M., Blanco, V.O., Gonzalez, R.E., Graham, S.A., Zumberge, J.E., Wavrek, D.A., 2019. Identification of genetically distinct petroleum tribes in the Middle Magdalena Valley, Colombia. American Association of Petroleum Geologists Bulletin 103, 3003-3034.


Six distinct oil tribes were established using multivariate statistical analysis of source-related biomarker and isotopic ratios for 73 crude oil samples from the Middle Magdalena Valley (MMV), Colombia. These six tribes show a systematic distribution by both basin location and reservoir rock age and may originate from different source rocks or different organofacies of the same source rock. Biomarker and isotopic data further differentiate the tribes with respect to source rock depositional environment, lithology, organic matter type, and thermal maturity. The thermal maturity and reservoir interval for the northernmost tribe 5 suggest a middle Cretaceous Tablazo Formation source rock. In contrast, tribes 1 through 4 are likely derived from the primary regional source rock, the Upper Cretaceous La Luna Formation. However, we observe regional differences in bulk

properties, thermal maturity, terrigenous input, and oxicity between the four La Luna–derived oil tribes. In addition, tribe 3 appears to result from end-member mixing between tribes 2 and 4. Finally, the southernmost tribe 6 is the only oil with terrigenous character. Diamondoid analysis shows the presence of significant secondary cracking in the tribe 6 oil with low levels of cracking present in oil samples from tribes 1 and 2 in the central MMV. This suggests a more deeply buried nonmarine source along the western flank of the Andean Eastern Cordillera. The integration of chemometric, biomarker, and diamondoid analyses have improved our understanding of the MMV petroleum system and advocate for the presence of three or more source rock intervals within the basin.


https://doi.org/10.1038/s41598-019-54322-8

Water has many roles in the context of life on Earth, however throughout the universe, other liquids may be able to support the emergence of life. We looked at the ability of amino acids, peptides, a depsipeptide, and proteins to partition into a non-polar decanol phase, with and without the addition of a phase transfer agent. Partitioning evaluated using UV detection, or with HPLC coupled to either charged aerosol detection or ESI-MS. For amino acids and short peptides, phase transfer agents were used to move the biomolecules to the decanol phase, and this transfer was pH dependent. For larger molecules, phase transfer agents did not seem to affect the transfer. Both the depsipetide, valinomycin, and the protein Taq DNA polymerase had solubility in the decanol phase. Additionally, valinomycin appeared to retain its biological ability to bind to potassium ions. These results show that most terrestrial biological molecules are not compatible with non-polar solvents, but it is possible to find and perhaps evolve polymers that are functional in such phases.

Thompson, J.W., Adams, K.J., Adamski, J., Asad, Y., Borts, D., Bowden, J.A., Byram, G., Dang, V., Dunn, W.B., Fernandez, F., Fiehn, O., Gaul, D.A., Hühmer, A.F.R., Kalli, A., Koal, T., Koeniger, S., Mandal, R., Meier, F., Naser, F.J., O’Neil, D., Pal, A., Patti, G.J., Pham-Tuan, H., Prehn, C., Raynaud, F.I., Shen, T., Southam, A.D., St. John-Williams, L., Sulek, K., Vasilopoulou, C.G., Viant, M., Winder, C.L., Wishart, D., Zhang, L., Zheng, J., Moseley, M.A., 2019. International ring trial of a high resolution targeted metabolomics and lipidomics platform for serum and plasma analysis. Analytical Chemistry 91, 14407-14416.


A challenge facing metabolomics in the analysis of large human cohorts is the cross-laboratory comparability of quantitative metabolomics measurements. In this study, 14 laboratories analyzed various blood specimens using a common experimental protocol provided with the Biocrates AbsoluteIDQ p400HR kit, to quantify up to 408 metabolites. The specimens included human plasma and serum from male and female donors, mouse and rat plasma, as well as NIST SRM 1950 reference plasma. The metabolite classes covered range from polar (e.g., amino acids and biogenic amines) to nonpolar (e.g., diacyl- and triacyl-glycerols), and they span 11 common metabolite classes. The manuscript describes a strict system suitability testing (SST) criteria used to evaluate each laboratory’s readiness to perform the assay, and provides the SST Skyline documents for public dissemination. The study found approximately 250 metabolites were routinely quantified in the sample types tested, using Orbitrap instruments. Interlaboratory variance for the NIST SRM-1950 has a median of 10% for amino acids, 24% for biogenic amines, 38% for acylcarnitines, 25% for glycerolipids, 23% for glycerophospholipids, 16% for cholesteryl esters, 15% for sphingolipids, and 9% for hexoses. Comparing to consensus values for NIST SRM-1950, nearly 80% of comparable analytes demonstrated bias of <50% from the reference value. The findings of this study result in recommendations of best practices for system suitability, quality control, and calibration. We demonstrate that with appropriate controls, high-resolution metabolomics can provide accurate results with good precision across laboratories, and the p400HR therefore is a reliable approach for generating consistent and comparable metabolomics data.

Thorne, R.J., Sundseth, K., Bouman, E., Czarnowska, L., Mathisen, A., Skagestad, R., Stanek, W., Pacyna, J.M., Pacyna, E.G., 2020. Technical and environmental viability of a European CO2 EOR system. International Journal of Greenhouse Gas Control 92, 102857.


Captured CO2 from large industrial emitters may be used for enhanced oil recovery (EOR), but as of yet there are no European large-scale EOR systems. Recent implementation decisions for a Norwegian carbon capture and storage demonstration will result in the establishment of a central CO2 hub on the west-coast of Norway and storage on the Norwegian Continental Shelf. This development may continue towards a large-scale operation involving European CO2 and CO2 EOR operation. To this end, a conceptual EOR system was developed here based on an oxyfuel power plant located in Poland that acted as a source for CO2, coupled to a promising oil field located on the Norwegian Continental Shelf. Lifecycle assessment was subsequently used to estimate environmental emissions indicators. When averaged over the operational lifetime, results show greenhouse gas (GHG) emissions of 0.4 kg CO2-eq per kg oil (and n kWh associated electricity) produced, of which 64 % derived from the oxyfuel power plant. This represents a 71 % emission reduction when compared to the same amount of oil and electricity production using conventional technology. Other environmental impact indicators were increased, showing that this type of CO2 EOR system may help reach GHG reduction targets, but care should be taken to avoid problem shifting.

Tong, H., Zhang, Y., Filippi, A., Wang, T., Li, C., Liu, F., Leppla, D., Kourtchev, I., Wang, K., Keskinen, H.-M., Levula, J.T., Arangio, A.M., Shen, F., Ditas, F., Martin, S.T., Artaxo, P., Godoi, R.H.M., Yamamoto, C.I., de Souza, R.A.F., Huang, R.-J., Berkemeier, T., Wang, Y., Su, H., Cheng, Y., Pope, F.D., Fu, P., Yao, M., Pöhlker, C., Petäjä, T., Kulmala, M., Andreae, M.O., Shiraiwa, M., Pöschl, U., Hoffmann, T., Kalberer, M., 2019. Radical formation by fine particulate matter associated with highly oxygenated molecules. Environmental Science & Technology 53, 12506-12518.


Highly oxygenated molecules (HOMs) play an important role in the formation and evolution of secondary organic aerosols (SOA). However, the abundance of HOMs in different environments and their relation to the oxidative potential of fine particulate matter (PM) are largely unknown. Here, we investigated the relative HOM abundance and radical yield of laboratory-generated SOA and fine PM in ambient air ranging from remote forest areas to highly polluted megacities. By electron paramagnetic resonance and mass spectrometric investigations, we found that the relative abundance of HOMs, especially the dimeric and low-volatility types, in ambient fine PM was positively correlated with the formation of radicals in aqueous PM extracts. SOA from photooxidation of isoprene, ozonolysis of α- and β-pinene, and fine PM from tropical (central Amazon) and boreal (Hyytiälä, Finland) forests exhibited a higher HOM abundance and radical yield than SOA from photooxidation of naphthalene and fine PM from urban sites (Beijing, Guangzhou, Mainz, Shanghai, and Xi’an), confirming that HOMs are important constituents of biogenic SOA to generate radicals. Our study provides new insights into the chemical relationship of HOM abundance, composition, and sources with the yield of radicals by laboratory and ambient aerosols, enabling better quantification of the component-specific contribution of source- or site-specific fine PM to its climate and health effects.

Toor, M., Kumar, S.S., Malyan, S.K., Bishnoi, N.R., Mathimani, T., Rajendran, K., Pugazhendhi, A., 2020. An overview on bioethanol production from lignocellulosic feedstocks. Chemosphere 242, 125080.


Lignocellulosic ethanol has been proposed as a green alternative to fossil fuels for many decades. However, commercialization of lignocellulosic ethanol faces major hurdles including pretreatment, efficient sugar release and fermentation. Several processes were developed to overcome these challenges e.g. simultaneous saccharification and fermentation (SSF). This review highlights the various ethanol production processes with their advantages and shortcomings. Recent technologies such as singlepot biorefineries, combined bioprocessing, and bioenergy systems with carbon capture are promising. However, these technologies have a

lower technology readiness level (TRL), implying that additional efforts are necessary before being evaluated for commercial availability. Solving energy needs is not only a technological solution and interlinkage of various factors needs to be assessed beyond technology development.

Tripathi, R., Kumar, P., Ghosh, S., Nagalingam, J., Singh, H., 2019. Culture based investigations of key microbial functional groups in gas hydrate bearing sediments of the Krishna-Godavari Basin in offshore India. Marine and Petroleum Geology 108, 397-406.


Results of National Gas Hydrate Program-02 (NGHP-02) expedition have confirmed the resource potential of sand-hosted gas hydrate accumulations in the deep offshore of Krishna-Godavari Basin (KG Basin). NGHP-02 has identified two types of gas hydrate accumulations: one is thick, layer-type units developed in sand-rich facies at depths of a few 100 m below sea floor (mbsf), and the other, fracture type unit of variable thickness at shallow depths. Fracture-type and Layer-type gas hydrates were observed in Areas B, C, and E in the KG Basin as defined under NGHP-02. The importance of each type of gas hydrate occurrence as discovered during NGHP-02 has led to the need for microbial profiling. Different classes of microbes, anaerobic fermentative microbes (AFM), methanotrophs and sulphate reducing bacteria (SRB) were studied to understand the microbial system for biogenic gas generation in sedimentary sequences encountered in eight core holes (4 in Area B, 3 in Area C and 1 in Area E) as established during NGHP-02. This study reveals the availability of highest concentration of methane generating microbes that are closely associated with high total organic carbon (TOC) content in the identified gas hydrate bearing sedimentary units cored in each borehole. The presence of microbial consortia for methane generation through both processes, of reduction of CO2 and fermentation of formate/acetate has been confirmed. Stratigraphic correlation between drill sites have also been generated to better understand the spatial relationship of various microbial processes. An observation from the study, is that the entire late Miocene age sediments has potential to generate biogenic gas in Holes NGHP-02-05B, −17B, −22B and −23B. Late to early Pleistocene age sediments are showing methane generating activity in Holes NGHP-02-01C, −08B and −09B, while early Pleistocene to late Pliocene age sediments contains methane generating microbes in Holes NGHP-02-05B, −17B, −19B, −22B and −23B. The existence of methane generating biogenic microbial system in Areas B, C and E of KG Basin has been confirmed.

Tsaousis, A.D., 2019. On the origin of iron/sulfur cluster biosynthesis in eukaryotes. Frontiers in Microbiology 10, 2478. doi: 10.3389/fmicb.2019.02478.


Iron and sulfur are indispensable elements of every living cell, but on their own these elements are toxic and require dedicated machineries for the formation of iron/sulfur (Fe/S) clusters. In eukaryotes, proteins requiring Fe/S clusters (Fe/S proteins) are found in or associated with various organelles including the mitochondrion, endoplasmic reticulum, cytosol, and the nucleus. These proteins are involved in several pathways indispensable for the viability of each living cell including DNA maintenance, protein translation and metabolic pathways. Thus, the formation of Fe/S clusters and their delivery to these proteins has a fundamental role in the functions and the evolution of the eukaryotic cell. Currently, most eukaryotes harbor two (located in cytosol and mitochondrion) or three (located in plastid) machineries for the assembly of Fe/S clusters, but certain anaerobic microbial eukaryotes contain sulfur mobilization (SUF) machineries that were previously thought to be present only in archaeal linages. These machineries could not only stipulate which pathway was present in the last eukaryotic common ancestor (LECA), but they could also provide clues regarding presence of an Fe/S cluster machinery in the proto-eukaryote and evolution of Fe/S cluster assembly machineries in all eukaryotes.

Uchida, S., Lin, J.-S., Myshakin, E.M., Seol, Y., Boswell, R., 2019. Numerical simulations of sand migration during gas production in hydrate-bearing sands interbedded with thin mud layers at site NGHP-02-16. Marine and Petroleum Geology 108, 639-647.


The geomechanical behavior of gas hydrate-bearing sands during gas production is complex, involving changes in hydrate-dependent mechanical characteristics and also redistribution of stresses carried by the hydrate. When an interbedded mud layer is present, the complex response of the hydrate-bearing sediments is more pronounced because hydrate dissociation tends to occur preferentially in the sands adjacent to the hydrate-free mud layer, which can act as a heat source. This leads to non-uniform sediment deformation and potentially to shearing deformation along the sand/mud layers. In addition, since the hydrate-bearing sand permeability becomes far greater than the mud permeability with hydrate dissociation, a greater hydraulic gradient may exist along the interface between the sand/mud layers. These two behaviors may contribute to sand migration and thus a thorough study on the effect of a thin interbedded mud layer on the extent of sand migration is necessary. This paper presents numerical sand migration modeling of sand/mud interbedded hydrate-bearing sediments found at Site NGHP-02-16, one of 25 sites drilled as a part of National Gas Hydrate Program Expedition 02 (NGHP-02) in the offshore of India, subjected to depressurization. For a comparison and better understanding, simulation of homogeneous hydrate-bearing sediments is also conducted. It is found that greater sand migration occurs when the interbedded mud layer is present because of greater shearing deformation and greater pressure gradients at sand-mud interface.

Umhau, B.P., Benitez-Nelson, C.R., Close, H.G., Hannides, C.C.S., Motta, L., Popp, B.N., Blum, J.D., Drazen, J.C., 2019. Seasonal and spatial changes in carbon and nitrogen fluxes estimated using 234Th:238U disequilibria in the North Pacific tropical and subtropical gyre. Marine Chemistry 217, 103705.


Particle dynamics are an essential component of global ocean biogeochemistry as they transport essential nutrients, carbon, and other reactive elements and compounds from the surface ocean to depth in the water column. The North Pacific Ocean is characterized by spatial and temporal variations in particle export mediated by a diverse food web and variations in environmental conditions, such as oxygenation. Here we explored temporal variability in the downward flux of particulate carbon (PC) and nitrogen (PN) using 238U-234Th disequilibria, sediment traps and in situ pumps in winter, spring and summer at the time-series site Station ALOHA, a region characterized by a well-defined summer export pulse that influences the composition and structure of the biological community within the mesopelagic zone. We further explored spatial variability in PC and PN fluxes along a latitudinal gradient (17.5°-5°N x 150°W) that transitions from a low to high productivity region influenced by equatorial upwelling, with several stations further characterized by a shallow (~ 130 m) oxygen minimum zone. Winter PC and PN fluxes at 150 m at Station ALOHA were low, while summer and spring fluxes were significantly higher, coinciding with a seasonal export pulse associated with diazotrophs. PC and PN fluxes along the 155°W transect were also low at 150 m and similar to those measured at Station ALOHA in winter. At Station ALOHA zooplankton impart a greater influence over both small and large PC (and PN) fluxes in February relative to September or May, when heterotrophic bacteria play a proportionally larger role in particle remineralization and cycling. Along the transect stations, PC fluxes were too low to discern any clear trends with latitude, likely due to El Niño conditions at the time of sampling. Where vertical water column profiles of PC and PN fluxes were available, PC (and PN) fluxes were found to peak in the subsurface at 8°N (50 m) and 5°N (75 m) with zooplankton grazing and microbial remineralization following patterns similar to those found in February at Station ALOHA. Combined, these results support the hypothesis that small and large particles contribute to mesopelagic carbon demand depending on season, with smaller particles having greater contributions to mesopelagic food webs when surface derived particle export is low.

Uribe-Lorío, L., Brenes-Guillén, L., Hernández-Ascencio, W., Mora-Amador, R., González, G., Ramírez-Umaña, C.J., Díez, B., Pedrós-Alió, C., 2019. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. MicrobiologyOpen 8, e893.

https://doi.org/10.1002/mbo3.893

We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of

temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.


https://doi.org/10.1038/s41598-019-52863-6

The end of the Late Palaeozoic Ice Age (LPIA) ushered in a period of significant change in Earth’s carbon cycle, demonstrated by the widespread occurrence of coals worldwide. In this study, we present stratigraphically constrained organic stable carbon isotope (δ13Corg) data for Early Permian coals (312 vitrain samples) from the Moatize Basin, Mozambique, which record the transition from global icehouse to greenhouse conditions. These coals exhibit a three-stage evolution in atmospheric δ13C from the Artinskian to the Kungurian. Early Kungurian coals effectively record the presence of the short-lived Kungurian Carbon Isotopic Excursion (KCIE), associated with the proposed rapid release of methane clathrates during deglaciation at the terminus of the Late Palaeozoic Ice Age (LPIA), with no observed disruption to peat-forming and terrestrial plant communities. δ13Corg variations in coals from the Moatize Basin are cyclic in nature on the order of 103–105 years and reflect changes in δ13Corg of ~±1‰ during periods of stable peat accumulation, supporting observations from Palaeozoic coals elsewhere. These cyclic variations express palaeoenvironmental factors constraining peat growth and deposition, associated with changes in base level. This study also demonstrates the effectiveness of vitrain in coal as a geochemical tool for recording global atmospheric change during the Late Palaeozoic.

Van Hale, R.J., Holder, P.W., Harrison, J.D.S., Frew, R.D., 2019. Extending the limit of measurement for dual H and O isotope ratios using thermolysis. Analytical Chemistry 91, 13367-13371.


Hydrogen and oxygen isotope ratios are of use to determine the origin of matter. Thermolysis is used to convert matter to H2 and CO gases, which are the respective substrates for measurement of these two isotope ratios, using isotope ratio mass spectrometry (IRMS). This work was done in response to the need for analysis of small invasive insects, requiring a decrease in the limit of measurement for isotope ratiometry of hydrogen and oxygen, while determining both isotope ratios on the same sample. Miniaturization of a thermolysis reactor using commercially available components is presented that results in improvement in the limit of measurement for both hydrogen and oxygen isotope ratios. δ2H was determined on 0.4 μg of H and δ18O determined on 5 μg of O with precisions of 3 mUr and 0.7 mUr, respectively. To extend the usable sample size range or increase the resolution of sampling gives obvious advantages in forensic and environmental sciences. The technique has been applied to determining the natural origin of Tephritidae fruit flies for which only the wing is suitable for analysis and provides just 60 μg of material for analysis.

van Santen, J.A., Jacob, G., Singh, A.L., Aniebok, V., Balunas, M.J., Bunsko, D., Neto, F.C., Castaño-Espriu, L., Chang, C., Clark, T.N., Cleary Little, J.L., Delgadillo, D.A., Dorrestein, P.C., Duncan, K.R., Egan, J.M., Galey, M.M., Haeckl, F.P.J., Hua, A., Hughes, A.H., Iskakova, D., Khadilkar, A., Lee, J.-H., Lee, S., LeGrow, N., Liu, D.Y., Macho, J.M., McCaughey, C.S., Medema, M.H., Neupane, R.P., O’Donnell, T.J., Paula, J.S., Sanchez,

L.M., Shaikh, A.F., Soldatou, S., Terlouw, B.R., Tran, T.A., Valentine, M., van der Hooft, J.J.J., Vo, D.A., Wang, M., Wilson, D., Zink, K.E., Linington, R.G., 2019. The Natural Products Atlas: An open access knowledge base for microbial natural products discovery. ACS Central Science 5, 1824-1833.

https://doi.org/10.1021/acscentsci.9b00806

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

Vaníčková, L., Pompeiano, A., Maděra, P., Massad, T.J., Vahalík, P., 2020. Terpenoid profiles of resin in the genus Dracaena are species specific. Phytochemistry 170, 112197.


Dragon's blood is the colloquial name for the red resin produced by tree species in the genus Dracaena (Asparagaceae), and the resin is directly involved in plant defensive mechanisms against pathogen and herbivore attack. It is also widely used in traditional folk medicine due to its antiviral, antimicrobial and antitumor activities. In the present work, a method using solid phase microextraction combined with two-dimensional gas chromatography with time-of-flight mass spectrometric detection was developed for the analysis of resin from five Dracaena species, namely Dracaena cinnabari Balf. f., D. serrulata Baker, D. ombet Heuglin ex Kotschy & Peyr., D. draco subsp. draco, and D. draco subsp. ajgal. Twenty terpenoid components in the resins of the five species were identified after comparative study of the volatile metabolite profiles. Monoterpenes were found to be species specific, and the observed differences might be further investigated as a possible means of identifying chemotaxonomic markers. In addition, for the first time, we describe the terpenoid volatile profiles of D. ombet and D. serrulata resins.

Vatandoust, M., Faghih, A., Asadi, S., Azimzadeh, A.M., Heidarifard, M.H., 2020. Study of hydrocarbon generation and 1D-2D modeling of hydrocarbon migration at the Karanj and Parsi oilfields, Southern Dezful Embayment, SW Iran. Marine and Petroleum Geology 113, 104095.


This study is a 2D basin modeling to determine the petroleum system (i.e. Cretaceous-Neogene play) of the Karanj and Parsi oilfields in the Southern Dezful Embayment, SW Iran. This system is characterized by occurrence of source rocks of Middle Cretaceous, Late Cretaceous and Paleocene to Eocene (Kazhdumi, Pabdeh and Gurpi Formation), reservoirs of Upper Cretaceous and Late Oligocene–Early Miocene (Ilam-Sarvak and Asmari formations), and seals of Paleocene and Miocene (Pabdeh and Gachsaran Formation). Considering temperature, transformation ratio and vitrinite reflectance, the maturity of source rocks (Kazhdumi, Pabdeh and Gurpi Formation) was investigated. A maturity history analysis showed that the maturity of Kazhdumi, Pabdeh and Gurpi Formation started during 70–60 and 4 Ma, respectively. Generation and expulsion of hydrocarbons started ~16 Ma in the Kazhdumi Formation and ~3 Ma in the Pabdeh Formation that continued up to the present. The analysis of the transformation ratio indicates transformation of significant amounts of Kazhdumi source rocks for generating hydrocarbons. Migration of hydrocarbons from the Kazhdumi Formation is mainly vertically upward. From Pabdeh Formation migration is both vertically upward (to the Asmari reservoir) and downwards (to the Ilam-Sarvak reservoir). However, some local traps have formed due to the hydrocarbon accumulation above the faults. Our results reveal that petroleum generation, migration and entrapment occurred at proper timing which facilitated the migration of hydrocarbons and their accumulation in the reservoirs.

Veldkornet, D., Rajkaran, A., Paul, S., Naidoo, G., 2020. Oil induces chlorophyll deficient propagules in mangroves. Marine Pollution Bulletin 150, 110667.

http://www.sciencedirect.com/science/article/pii/S0025326X1930815X

In Australia, some trees of the mangrove, Avicennia marina, growing in a chronic oil polluted site, produce chlorophyll deficient (albino) propagules. We tested the hypothesis that albinism was due to an oil-induced mutant allele that controls photosynthesis. We determined whether there are genetic differences between normal and chlorophyll deficient propagules. Four gene regions (nuclear 18S–26S cistron; chloroplast - trnH-psbA, rsp16 and matK) were sequenced and analysed for normal and albino propagules. Mutations occurred in both nuclear (ITS) and coding chloroplast (matK) genes of albino propagules. There were 10 mutational differences between normal and albino propagules in the matK samples. Analysis of molecular variation (AMOVA) of the matK dataset indicated highly significant genetic differentiation between normal and albino propagules. Our study suggests for the first time that PAHs from a chronic oil polluted site resulted in mutations in both nuclear and chloroplast genes, resulting in the production of albino propagules.

Velivetskaya, T.A., Ignatiev, A.V., Yakovenko, V.V., Vysotskiy, S.V., 2019. An improved femtosecond laser-ablation fluorination method for measurements of sulfur isotopic anomalies (∆33S and ∆36S) in sulfides with high precision. Rapid Communications in Mass Spectrometry 33, 1722-1729.


Rationale: Measurements of the multiple sulfur isotopic composition (δ34S, δ33S and δ36S values) of ancient sedimentary sulfide are useful for clarifying and reconstructing the picture of the global sulfur cycle on the early Earth. The methods used for these measurements should provide a high level of precision for the determination of sulfur isotope mass‐independent anomalies (∆33S and ∆36S values). Here we propose some improvements to the earlier published femtosecond laser‐ablation fluorination method to make it suitable for measuring both ∆33S and ∆36S values in the Archean sedimentary sulfides with acceptable precision.

Methods: A new gas purification system for the laser‐ablation fluorination method has been developed. The design of this system is based on temperature‐controlled flow traps for cryogenic separation of SF6 gas from other fluorinated products produced by fluorination of sulfide minerals. Compared with the previous version of the purification system, the efficiency of SF6 purification was significantly improved, which in turn improved

the precision of the method for in situ GC/IRMS measurements of 36S/32S ratios (and determination of ∆36S values).

Results: The improved method was tested using IAEA reference materials, as well as samples of natural pyrite with zero and non‐zero sulfur isotope anomalies. For samples of ~12–13 nmol SF6 (optimal size), the overall precision of the method is ±0.03‰ for ∆33S values and ±0.27‰ for ∆36S values. This level of precision is satisfactory to examine the sulfur isotope anomalies in the rock.

Conclusions: The improved femtosecond laser‐ablation fluorination method is applicable for in situ measurements of δ34S, ∆33S and ∆36S values in sulfide minerals.

Vellekoop, J., Woelders, L., Sluijs, A., Miller, K.G., Speijer, R.P., 2019. Phytoplankton community disruption caused by latest Cretaceous global warming. Biogeosciences 16, 4201-4210.


Phytoplankton responses to a ∼350 kyr (kiloyear) long phase of gradual late Maastrichtian (latest Cretaceous) global warming starting at ∼66.4 Ma can provide valuable insights into the long-term influences of global change on marine ecosystems. Here we perform micropaleontological analyses on three cores from the New Jersey paleoshelf to assess the response of phytoplankton using cyst-forming dinoflagellates and benthic ecosystems using benthic foraminifera. Our records show that this latest Maastrichtian warming event (LMWE), characterized by a 4.0±1.3 ∘C warming of sea surface waters on the New Jersey paleoshelf, resulted in a succession of nearly monospecific dinoflagellate-cyst assemblages, dominated by the species Palynodinium grallator. This response, likely triggered by the combination of warmer and seasonally thermally stratified seas, appears to have been more intense at offshore sites than at nearshore sites. The LMWE, and related dinoflagellate response, is associated with an impoverished benthic ecosystem. A wider geographic survey of literature data reveals that the dominance of P. grallator is a marker for the LMWE throughout the northern midlatitudes. While the dinocyst assemblage returned to a stable, normal marine community in the last tens of thousands of years of the Maastrichtian, benthic foraminiferal diversity appears to have remained slightly suppressed. Increased ecosystem stress during the latest Maastrichtian potentially primed global ecosystems for the subsequent mass extinction following the Cretaceous Paleogene (K–Pg) boundary Chicxulub impact.



Increased economic activity in the Arctic may increase the risk of oil spills. Yet, little is known about the degradation of oil spills by solar radiation and the impact of nutrient limitation on oil biodegradation under Arctic conditions. We deployed adsorbents coated with thin oil films for up to 4 months in a fjord in SW Greenland to simulate and investigate in situ biodegradation and photo-oxidation of dispersed oil droplets. Oil compound depletion by dissolution, biodegradation, and photo-oxidation was untangled by gas chromatography–mass spectrometry-based oil fingerprinting. Biodegradation was limited by low nutrient concentrations, reaching 97% removal of nC13–26-alkanes only after 112 days. Sequencing of bacterial DNA showed the slow development of a bacterial biofilm on the oil films predominated by the known oil degrading bacteria Oleispira, Alkanindiges and Cycloclasticus. These taxa could be related to biodegradation of shorter-chain (≤C26) alkanes, longer-chain (≥C16) and branched alkanes, and polycyclic aromatic compounds (PACs), respectively. The combination of biodegradation, dissolution, and photo-oxidation depleted most PACs at substantially faster rates than the biodegradation of alkanes. In Arctic fjords during summer, nutrient limitation may severely delay oil biodegradation, but in the photic zone, photolytic transformation of PACs may play an important role.

Verlhac, B., Bachellier, N., Garnier, L., Ormaza, M., Abufager, P., Robles, R., Bocquet, M.L., Ternes, M., Lorente, N., Limot, L., 2019. Atomic-scale spin sensing with a single molecule at the apex of a scanning tunneling microscope. Science 366, 623-627.


Abstract: Recent advances in scanning probe techniques rely on the chemical functionalization of the probe-tip termination by a single molecule. The success of this approach opens the prospect of introducing spin sensitivity through functionalization by a magnetic molecule. We used a nickelocene-terminated tip (Nc-tip), which offered the possibility of producing spin excitations on the tip apex of a scanning tunneling microscope (STM). When the Nc-tip was 100 picometers away from point contact with a surface-supported object, magnetic effects could be probed through changes in the spin excitation spectrum of nickelocene. We used this detection scheme to simultaneously determine the exchange field and the spin polarization of iron atoms and cobalt films on a copper surface with atomic-scale resolution.

Editor's Summary: Single molecules sense spin. Imaging surface magnetism, and, in particular, spin excitations of adsorbed molecules or films, is challenging. Verlhac et al. demonstrate spin-sensing capability by using the magnetic exchange interaction between a surface sample and the spin-excited states of a nickelocene molecule attached to a scanning tunneling microscope tip. The spatial dependence of the exchange field at the atomic scale enabled imaging of magnetic corrugation with atomic-scale lateral resolution for iron atoms and small islands of cobalt atoms absorbed on nonmagnetic copper surfaces.

Verma, A., Chauhan, G., Ojha, K., Padmanabhan, E., 2019. Characterization of nano-Fe2O3-stabilized polymer-free foam fracturing fluids for unconventional gas reservoirs. Energy & Fuels 33, 10570-10582.


The present investigation is aimed at formulating a stable foam for fracturing of unconventional reservoirs through selective application of various combinations of nanoparticles and surfactants. Ferric oxide nanoparticles are proposed for the first time to enhance the thermal stability of the foam fluid for hydraulic fracturing. Addition of ferric oxide nanoparticles up to a concentration of 0.5 wt % as a foam stabilizer to the mixture of surfactants (SDBS and CAPB) improved the foam rheology and enhanced thermal stability to 52% at 80 °C. A morphological study of foam bubbles through confocal laser scanning and microscopic analyses validated the experimental results in improved stability and reduction in film drainage time through adsorption of nanoparticles on the bubble interfaces. In addition, nanostabilized foam bubbles showed enhanced viscosity and a satisfactory proppant settling velocity. Consequently, these above favorable outcomes help in improving proppant suspension capacity and efficient proppant transport through foam fluid for the fracturing job of unconventional reservoirs.

Vickers, M.L., Price, G.D., Jerrett, R.M., Sutton, P., Watkinson, M.P., FitzPatrick, M., 2019. The duration and magnitude of Cretaceous cool events: Evidence from the northern high latitudes. GSA Bulletin 131, 1979-1994.

https://doi.org/10.1130/B35074.1

The Early Cretaceous (145–100 Ma) was characterized by long-term greenhouse climates, with a reduced equatorial to polar temperature gradient, although an increasingly large body of evidence suggests that this period was punctuated by episodic global “cold snaps.” Understanding climate dynamics during this high-atmospheric CO2 period of Earth’s history may have significant impact on how we understand climatic feedbacks and predict future global climate changes under an anthropogenically-driven high-pCO2 atmosphere. This study utilizes facies analysis to constrain the paleobathymetry of Lower Cretaceous glendonites—a pseudomorph after ikaite, a mineral that forms naturally at 7 °C or lower—from two paleo-high-latitude (60–70°N) sites in Svalbard, Arctic Norway, to infer global climatic changes during the Early Cretaceous. The original ikaite formed in the offshore transition zone of a shallow marine shelf at water depths of <100 m, suggesting mean annual water temperatures of ≤7 °C at these depths at 60–70°N. We correlate glendonite-bearing horizons from Lower Cretaceous successions around the globe using carbon isotope stratigraphy, in

conjunction with the pre-existing biostratigraphic framework, in order to infer northern hemispheric to global climatic cooling. A distinct interval of glendonites in the Northern Hemisphere, from sites >60°N, spans the late Berriasian to earliest Barremian (at least 8.6 m.y.), significantly prolonging the duration of the previously hypothesized Valanginian cold snap (associated with the “Weissert Event”). Widespread glendonites occur again in late Aptian and extend to the early Albian, in both hemispheres, corroborating other proxy evidence for late Aptian cooling. The glendonites from Svalbard suggest that Cretaceous cold episodes were characterized with high latitude (>60°N) shallow water temperatures that are consistent with the existence of a small northern polar ice cap at this time.

Vinogradoff, V., Le Guillou, C., Bernard, S., Viennet, J.C., Jaber, M., Remusat, L., 2020. Influence of phyllosilicates on the hydrothermal alteration of organic matter in asteroids: Experimental perspectives. Geochimica et Cosmochimica Acta 269, 150-166.


The origin of the diverse organic compounds present in carbonaceous chondrites (CC) remains uncertain. We aim at investigating the role that hydrothermal alteration may have had on the molecular evolution of organic matter (OM). In particular, within CC matrices, OM is intimately embedded within phyllosilicates down to the nanometer scale, which raises the question of the influence of phyllosilicates on OM transformation during hydrothermal alteration on parent bodies. We conducted hydrothermal experiments at 150 °C and alkaline pH, using a well-known molecule present in processed interstellar ice analogues, the hexamethylenetetramine (HMT), in the presence of Al- and Fe-rich smectites. Experimental products were characterized by gas chromatography mass spectrometry, infrared spectroscopy, X-ray diffraction and synchrotron-based X-ray absorption near edge structure spectroscopy. Within 31 days, the HMT + smectites + H2O system leads to (1) the formation of a diverse suite of soluble organic compounds, yet less abundant and less complex than in the absence of smectite, (2) carbon-rich smectite residues (3.8 wt.% and 2.6 wt.% of carbon for the Al- and Fe-rich smectite residues, respectively). In addition, the abundance and molecular composition of the final organic compounds depend on the nature of the phyllosilicate (Al vs. Fe-smectite). Various and complex interaction mechanisms could occur between OM and smectite. Physisorption, chemisorption and intercalation processes have likely entrapped a significant portion of the organic compounds, thereby altering their chemical evolution. The present work demonstrates that the presence and the nature of phyllosilicates influences the reaction pathways of organic compounds during hydrothermal alteration and that the presence of organic compounds may impact the mineral assemblage. This could have had significant importance for the co-evolution of OM and mineral phases in primitive bodies during hydrothermal alteration.

Vinson, D.S., Blair, N.E., Ritter, D.J., Martini, A.M., McIntosh, J.C., 2019. Carbon mass balance, isotopic tracers of biogenic methane, and the role of acetate in coal beds: Powder River Basin (USA). Chemical Geology 530, 119329.


A multi-isotope (C, H, O) investigation of biogenic gas (δ13C−CH4, δ13C−CO2, δD−CH4) and coal bed waters (δD, δ18O, δ13C-DIC, δ13C-acetate) was conducted along a ∼25-km basinward sampling transect in the Powder River Basin (PRB) in Wyoming and Montana (USA) to address inconsistencies among isotope fingerprinting techniques and to apply mass balance isotope modeling to biogenic coalbed methane (CBM). Results include the first published compound-specific δ13C-acetate values from a natural biogenic CBM system, providing new constraints on acetate’s role in biogenic CH4 generation. Coal bed water chemistry is anoxic and dominated by Na+ and HCO3

−, with high alkalinity concentrations (14.8–33.0 meq/L). The deep basin interior environment contains sulfate-free, Na+−HCO3

−-dominated waters exhibiting signs of methanogenesis. CH4 and CO2 generally become 13C-enriched from the shallow basin edge to the deep basin interior (δ13C−CH4 −78.2 to −56.2‰ and δ13C−CO2 -24.7 to 4.7‰). Also, compound-specific δ13C-acetate is more positive in the basin interior compared to the basin edge setting (range −34.3 to −15.1‰). Using a steady-state mass balance isotope model, the observed variations in δ13C-CH4 and δ13C-CO2 can be explained in terms of the favorability of methanogenesis (fCH4) relative to heterotrophic bacterially-mediated non-methanogenic pathways, such as bacterial sulfate

reduction, which compete with methanogenesis for substrates. At the basin interior, fCH4 exceeds 0.4, approaching its inferred limiting value hypothesized from the oxidation state of low-molecular weight compounds detected in PRB formation waters. Therefore, methanogenesis is likely a dominant biogeochemical pathway consuming substrates in the deeper coal beds. The basinward shift toward 13C-enriched acetate broadly indicates linkage between acetate, CH4, and CO2, and likely records acetate synthesis effects modified by methanogenic fractionation. These results suggest that acetate plays a role in methanogenesis in PRB coal beds (not necessarily a dominant role), while other C isotope and microbial evidence suggests that hydrogenotrophic methanogenesis is also a significant methane-producing pathway. The results of this study broadly suggest multiple viable methanogenic pathways and C cycling that affects acetate, a more complex view of coal bed geochemistry than implied by traditional C and H isotope fingerprinting of accumulated products (CH4, CO2) and coexisting water.

Vlaskin, M.S., Grigorenko, A.V., Kotelev, M.S., Kopitsyn, D.S., Mazurova, K.M., Ivanov, E.V., 2019. Composition and properties of microalgae biomass hydrothermal liquefaction products. Chemistry and Technology of Fuels and Oils 55, 373-377.

https://doi.org/10.1007/s10553-019-01041-5

Hydrothermal liquefaction of microalgae biomass at various temperatures was studied. The products were analyzed by thermogravimetry, elemental analysis, and gas-chromatography—mass-spectromeny. It was concluded that the temperature affected the product yield and composition. The quantitative contents of the major components in the gasoline fraction of the produced bio-oil were determined. The main components in the gasoline fraction were aromatic hydrocarbons, alkanes, and cycloalkanes. The hydrothermal processing products also contained significant quantities of phenols, organic sulfides, and nitrogenous organic compounds that prevented their direct use as fuel components. Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 4, pp. 8 – 10, July – August, 2019.

Vogel, A.L., Lauer, A., Fang, L., Arturi, K., Bachmeier, F., Daellenbach, K.R., Käser, T., Vlachou, A., Pospisilova, V., Baltensperger, U., Haddad, I.E., Schwikowski, M., Bjelić, S., 2019. A comprehensive nontarget analysis for the molecular reconstruction of organic aerosol composition from glacier ice cores. Environmental Science & Technology 53, 12565-12575.


Ice cores are climate archives suitable for the reconstruction of past atmospheric composition changes. Ice core analysis provides valuable insight into the chemical nature of aerosols and enables constraining emission inventories of primary emissions and of gas-phase precursors. Changes in the emissions of volatile organic compounds (VOCs) can affect formation rates and mechanisms as well as chemical composition of aerosols during the preindustrial era, key information for understanding aerosol climate effects. Here, we present an analytical method for the reconstruction of organic aerosol composition preserved in glacier ice cores. A solid-phase-extraction method, optimized toward oxidation products of biogenic VOCs, provides an enrichment factor of ∼200 and quantitative recovery for compounds of interest. We applied the preconcentration method on ice core samples from the high-alpine Fiescherhorn glacier (Swiss Alps), and used high-performance liquid chromatography coupled to high-resolution mass spectrometry as a sensitive detection method. We describe a nontarget analysis that screens for organic molecules in the ice core samples. We evaluate the atmospheric origin of the detected compounds in the ice by molecular-resolved comparison with airborne particulate matter samples from the nearby high-alpine research station Jungfraujoch. The presented method is able to shed light upon the history of the evolution of organic aerosol composition in the anthropocene, a research field in paleoclimatology with considerable potential.

Voglar, G.E., Zavadlav, S., Levanič, T., Ferlan, M., 2019. Measuring techniques for concentration and stable isotopologues of CO2 in a terrestrial ecosystem: A review. Earth-Science Reviews 199, 102978.


Measurements of carbon dioxide and their stable isotopes are propulsive research tool in ecology and environmental science as they can give us insight into carbon cycle. They are widely used to investigate both natural and anthropogenic carbon sources in the atmosphere, hydrosphere and geosphere, as well as the exchange between these reservoirs. In this paper, we provide a basic overview of two different analytical measurement techniques, isotope ratio mass spectrometry (IRMS) and laser-absorption spectroscopy (LAS) which have been developed and utilized for monitoring of CO2 isotopologues in ecosystem. We present the basics for each technique, however with the emphasis on LAS measurement technique we are targeting readers who are not familiar with this topic. A major objective of this paper is to illustrate the current value and future potential of various analytical instruments in a wide range of applications deployed in the terrestrial ecosystem. Finally, we draw a conclusion from recent research campaigns by presenting a decision tree to better understand and choose a correct application combination for a selected scale of ecosystem.

Vonk, J.E., Tank, S.E., Walvoord, M.A., 2019. Integrating hydrology and biogeochemistry across frozen landscapes. Nature Communications 10, 5377.

https://doi.org/10.1038/s41467-019-13361-5

Research has traditionally focused on atmospheric release of carbon from thawing permafrost, yet overlooked waterborne release pathways likely contribute significantly, especially in a warming Arctic. To address this knowledge gap and better constrain the fate of carbon in the North, we recommend inter-disciplinary efforts bridging physical, chemical and computational research.

Change is unfolding beneath the surface of frozen landscapes that affects the coupled water and carbon cycles, and thus the fate of permafrost carbon, at local to pan-arctic scales. Degrading permafrost alters landforms and subsurface hydraulic properties, which allows water to infiltrate and circulate more freely and deeply. With thaw, organic matter is released from the large reservoir of permafrost carbon and may be converted into greenhouse gases via decomposition, giving rise to the permafrost carbon feedback that intensifies warming. While this direct route to the atmosphere is most commonly studied, organic matter is also mobilized into waterways. The form (e.g. gaseous, dissolved, particulate), pathway, and magnitude of constituent release via waterways varies widely among different landscapes and hydrologic conditions. Decomposition of organic matter in aquatic systems may generate greenhouse gas release downstream of the source, whereas aquatic systems may also be a sink for carbon burial, attenuating the permafrost carbon feedback5. At the global scale, this so-called lateral flux of carbon rivals the combined magnitude of the terrestrial and oceanic sink for anthropogenic CO2. The contribution of lateral permafrost carbon mobilization to the changing Arctic carbon cycle is increasingly recognized but remains poorly quantified.

Vyviurska, O., Špánik, I., 2020. Assessment of Tokaj varietal wines with comprehensive two-dimensional gas chromatography coupled to high resolution mass spectrometry. Microchemical Journal 152, 104385.


Botrytised wines produced in Tokaj region belong to a special category of sweet wines described with a pleasant honey-like taste and a distinctive fruit flavour. Specific technological process of wine-making developed on macerating of noble-rotten berries in fermented juice or wine, results in alcoholic beverage indicated with the 'Protected Designation of Origin' label. A limited number of publications is devoted to analysis of Tokaj wines or by-products (e.g. individual varietal wines, essencia and must) which directly related to final characteristics of botrytized wine. A combination of two-dimensional gas chromatography connected to high-resolution mass spectrometry (GC × GC-HRTOFMS) offers enhanced separation and reliable identification of organic compounds presented in complex samples. In our study, this technique was applied to analyse varietal wines of the Tokaj wine region produced from three main grape cultivars (Furmint, Lipovina and Muscat Blanc à Petits Grains). The primary task was reliable separation and identification of low volatility compounds (acetamides, 2H-pyrrole- and 2H-pyran-based heterocyclic compounds and sulphur containing compounds) because of the lack of available information in this area. Thus, it revealed the presence of 1(3H)-isobenzofuranone, ethyl 1H-indole-3-acetate and 2-(methylmercapto)benzothiazole which were not previously detected in wine. Furthermore, trace aroma compounds (terpenoids and lactones) was quantified with modified

stir bar sorptive extraction method which provided LOD and LOQ values of 2.3 – 4.7 ng/L and 7.7 – 15.8 ng/L, respectively. Linear calibration dependencies with correlation coefficients varying between 0.960 – 0.996 were obtained.



Filamentous microfossils belonging to Cephalophytarion from the 850 Ma Bitter Springs Group have previously been used as key analogues in support of a biological interpretation for filamentous objects from the 3460 Ma Apex chert. Here we provide a new perspective on this interpretation by combining Raman data with correlative electron microscopy data from both Cephalophytarion and Apex specimens. We show that, when analysed at high spatial resolution, the Apex filaments bear no morphological resemblance to the younger Bitter Springs microfossils. Cephalophytarion filaments are shown to be cylindrical, comprising chains of box-like cells of approximately constant dimensions with lateral kerogenous walls and transverse kerogenous septa. They exhibit taphonomic shrinkage and folding, possess fine cylindrical sheaths and are permineralized by sub-micrometric quartz grains. They fulfil all established biogenicity criteria for trichomic microfossils. In contrast, Apex filaments do not possess lateral cell walls, are not cylindrical in nature, and vary considerably in diameter along their length. Their kerogenous carbon does not have a cell-like distribution and their chemistry is consistent with an origin as exfoliated phyllosilicate grains. This work demonstrates the importance of high-resolution data when interpreting the microstructure, and origins, of putative Precambrian microfossils.

Wade, L., 2019. Immigrants from the Middle East shaped Rome. Science 366, 673.


Two thousand years ago, the streets of Rome bustled with people from all over the ancient world. The empire's trade routes stretched from North Africa to Asia, and new immigrants poured in every day, both by choice and by force. Now, an ancient DNA study has shown those far-flung connections were written in the genomes of the Romans.

People from the city's earliest eras and from after the Western empire's decline in the fourth century C.E. genetically resembled other Western Europeans. But during the imperial period most sampled residents had Eastern Mediterranean or Middle Eastern ancestry. At that time, “Rome was like New York City … a concentration of people of different origins joining together,” says Guido Barbujani, a population geneticist at the University of Ferrara in Italy who wasn't involved in the study. “This is the kind of cutting-edge work that's starting to fill in the details [of history],” adds Kyle Harper, a Roman historian at the University of Oklahoma in Norman.

The study, on p. 708, traces 12,000 years of history using genomes from 127 people buried at 29 archaeological sites in and around the city of Rome. Alfredo Coppa, a physical anthropologist at Sapienza University of Rome, sought hundreds of samples from dozens of previously excavated sites. Ron Pinhasi of the University of Vienna extracted DNA from the skeletons' ear bones, and Jonathan Pritchard, a population geneticist at Stanford University, sequenced and analyzed their DNA.

The oldest genomes came from three hunter-gatherers who lived 9000 to 12,000 years ago and genetically resembled other hunter-gatherers in Europe at the time. Later genomes showed the Romans changed in step with the rest of Europe, as an influx of early farmers with ancestry from Anatolia (what is now Turkey) reshaped the genetics of the entire region some 9000 years ago.

But Rome went its own way from 900 B.C.E. to 200 B.C.E. That's when it grew from a small town into an important city, says Kristina Killgrove, a Roman bioarchaeologist at the University of North Carolina in Chapel Hill who wasn't involved in the study. During its growth, “probably a lot of migration [was] happening,” she

says—as the genomes of 11 individuals from this period confirm. Some people had genetic markers resembling those of modern Italians, whereas others had markers reflecting ancestry from the Middle East and North Africa.

That diversity increased even more as Rome became an empire. Between 27 B.C.E. and 300 C.E., the city was the capital of an empire of 50 million to 90 million people, stretching from North Africa to Britain to the Middle East. Its population grew to more than 1 million people. The genetic “diversity was just overwhelming,” Pinhasi says.

But people from certain parts of the empire were far more likely to move to the capital. The study suggests the vast majority of immigrants to Rome came from the East. Of 48 individuals sampled from this period, only two showed strong genetic ties to Europe. Another two had strong North African ancestry. The rest had ancestry connecting them to Greece, Syria, Lebanon, and other places in the Eastern Mediterranean and Middle East.

That makes sense, Harper says, because at the time, areas to the east of Italy were more populous than Europe; many people lived in big cities such as Athens and Alexandria. And Rome was connected to Greece and the Middle East by the Mediterranean Sea, which was far easier to traverse than overland routes through the Alps, he says.

“The genetic information parallels what we know from historical and archaeological records,” Killgrove says. She and others have identified individuals from imperial Roman cemeteries who likely didn't grow up in Rome, based on isotopes in their teeth that reflect the water they drank when young—though the studies couldn't show their precise origins. Ancient texts and words carved on tombstones also point to large populations of immigrants in the city, Harper says.

But once the empire split in two and the eastern capital moved to Constantinople (what is now Istanbul, Turkey) in the fourth century C.E., Rome's diversity decreased. Trade routes sent people and goods to the new capital, and epidemics and invasions reduced Rome's population to about 100,000 people. Invading barbarians brought in more European ancestry. Rome gradually lost its strong genetic link to the Eastern Mediterranean and Middle East. By medieval times, city residents again genetically resembled European populations.

“People perhaps imagine that the amount of migration we see nowadays is a new thing,” Pritchard says. “But it's clear from ancient DNA that populations have been mixing at really high rates for a long time.”

Wagner, S., Brandes, J., Spencer, R.G.M., Ma, K., Rosengard, S.Z., Moura, J.M.S., Stubbins, A., 2019. Isotopic composition of oceanic dissolved black carbon reveals non-riverine source. Nature Communications 10, 5064.

https://doi.org/10.1038/s41467-019-13111-7

A portion of the charcoal and soot produced during combustion processes on land (e.g., wildfire, burning of fossil fuels) enters aquatic systems as dissolved black carbon (DBC). In terms of mass flux, rivers are the main identified source of DBC to the oceans. Since DBC is believed to be representative of the refractory carbon pool, constraining sources of marine DBC is key to understanding the long-term persistence of carbon in our global oceans. Here, we use compound-specific stable carbon isotopes (δ13C) to reveal that DBC in the oceans is ~6‰ enriched in 13C compared to DBC exported by major rivers. This isotopic discrepancy indicates most riverine DBC is sequestered and/or rapidly degraded before it reaches the open ocean. Thus, we suggest that oceanic DBC does not predominantly originate from rivers and instead may be derived from another source with an isotopic signature similar to that of marine phytoplankton.

Waite, W.F., Jang, J., Collett, T.S., Kumar, P., 2019. Downhole physical property-based description of a gas hydrate petroleum system in NGHP-02 Area C: A channel, levee, fan complex in the Krishna-Godavari Basin offshore eastern India. Marine and Petroleum Geology 108, 272-295.


India's second National Gas Hydrate Program expedition, NGHP-02, collected logging while drilling and sediment core data in Area C offshore eastern India, to investigate controls on the distribution and peak saturations of methane gas hydrate occurrences in buried channel, levee and fan deposits. Physical property results are presented here for the four Area C coring sites: NGHP-02-07, targeting an upper continental-slope channel deposit; NGHP-02-08 and −09, targeting levee deposits on either side of a channel further downslope, and NGHP-02-05, targeting a sequence of fan deposits extending out from the slope base. Coarse-grained sediment exists at each site, but site-specific differences in clay distribution provide significant controls on the gas hydrate distribution and saturation. At NGHP-02-07, only the upper ∼4 m of a ∼42 m-thick, relatively low clay-content, coarse-grained interval is inferred to be gas hydrate-bearing. NGHP-02-07 has a relatively thin, high-permeability overburden seal, and methane-rich fluid likely leaks from the primary reservoir. NGHP-02-08's levee deposit seal is similarly permeable near the reservoir, but becomes less permeable toward the seafloor. Relative to NGHP-02-07, methane is retained more effectively in the NGHP-02-08 reservoir, but that reservoir is interbedded with layers of high clay-content, low gas hydrate saturation sediment, limiting the maximum gas hydrate content for NGHP-02-08. NGHP-02-09, the second levee deposit site, has a thicker, less permeable overburden than NGHP-02-08, combined with >50 m-thick, low clay-content reservoir sediments. Correspondingly, NGHP-02-09 has a thicker gas hydrate-bearing reservoir with consistently higher gas hydrate saturations than NGHP-02-08. NGHP-02-05 has abundant coarse-grained material spread over nearly the entire drilling interval, but the sediment is poorly sorted. Gas hydrate is distributed among several primarily coarse-grained layers, but gas hydrate saturations are limited by relatively high clay contents, and an overlying seal that is too thin and permeable to effectively retain methane in the reservoir.

Waite, W.F., Ruppel, C.D., Collett, T.S., Schultheiss, P., Holland, M., Shukla, K.M., Kumar, P., 2019. Multi-measurement approach for establishing the base of gas hydrate occurrence in the Krishna-Godavari Basin for sites cored during expedition NGHP-02 in the offshore of India. Marine and Petroleum Geology 108, 296-320.


The 2015 National Gas Hydrate Program of India's second expedition, NGHP-02, acquired logging and coring datasets for constraining the base of the gas hydrate occurrence zone (deepest GH) and the theoretical base of gas hydrate stability zone (BGHS). These data are used here for two primary goals: to constrain the deepest occurrence of gas hydrate relative to predicted stability limits and the observed BSR, and to characterize the nature of the contact between gas hydrate-bearing sediment and the underlying gas hydrate-free sediment. A consensus depth for the deepest GH is derived for each NGHP-02 coring site from downhole indicators of gas hydrate occurrence obtained from well-log electrical resistivity and acoustic data, pressure core compressional wave velocity measurements, and conventional core measurements of anomalously low temperatures. To establish the theoretical BGHS, models of gas hydrate phase stability with depth are compared with downhole temperature profiles derived from: 1) assuming a constant geothermal gradient consistent with downhole temperature measurements, and 2) assuming constant heat flow using a geotherm through the downhole temperature measurements and incorporating thermal conductivity calculated from borehole logging data. Although the deepest NGHP-02 GH occurrences are controlled at several sites by a lithologic boundary, most sites have deepest GH occurrences within a single coarse-grained lithology. Cutoffs within a single coarse-grained lithology, which occur for the primary NGHP-02 Area B gas hydrate reservoir, will inhibit pore-pressure drawdowns used to extract methane from gas hydrate as an energy resource.

Wang, A.K., Shao, P., 2019. Generation processes and geochemical analysis of simulated biogenic coalbed methane from lignite. Geochemistry International 57, 1295-1305.

https://doi.org/10.1134/S0016702919120115

Under laboratory conditions, biogenic CBM generation process from lignites simulated to study the geochemical producing process, as well as the possible generation pathways and mechanisms. Research results indicate that the generation process of biogenic CBM from lignite has at least two gas-generation peaks, and the gas-generation field in the first peak is higher than that in the second peak. During the first gas-generation peak, huminite is considered to be easily degraded by microorganism, while during the second gas-generation peak,

liptinite and inertiniteare degraded by methanogens. The compositions of carbon (δ13C1) and hydrogen (δD) isotope in methane show that the simulated bio-methane mainly generates from the pathway of acetic acid fermentation. The concentrations of CH4 and CO2 are mutually increasing and decreasing with the passage of experiment time, and produced CH4 enriched less 13C in the later period, both of which indicates that some CH4 may be from way of carbon dioxide reduction, especially in the end process. When lignite vitrinite reflectance (Ro) value increased, the gas-generation quantities decrease and CH4 concentrations decrease linearly, and there was a trend of decreasing δ13C1 value linearly at the same time. Identify the generation process and geochemical property of biogenic CBM from lignite is crucial to understanding and improving biogenic CBM production.

Wang, C., Zeng, J., Zhang, Z., Yu, Y., Wang, F., Liu, X., 2019. Geological characteristics and hydrocarbon potential of the detachment basin in the Baiyun depression, Pearl River Mouth Basin, South China Sea. Energy & Fuels 33, 10519-10532.


Hydrocarbon exploration in the deep-water area of the South China Sea is increasingly important. However, the Eocene strata, which are the primary source rock in the deep-water area of the Pearl River Mouth basin (PRMB), are poorly understood. This article studied the geological characteristics and hydrocarbon potential of the Eocene source rocks in the Baiyun Depression, which is the biggest and most important depression in the deep-water area of the PRMB. In the Eocene, the Baiyun Depression was an asymmetric rift basin that was controlled by the north-dipping detachment faults. A big freshwater lake existed in the study area and a huge delta developed in the northern gentle slope. The delta source rocks had higher total organic carbon and were greatly controlled by terrigenous organic matter input. They were type III kerogen and were likely to produce gas during maturation. The lacustrine source rocks were widely distributed in the center and south and had a higher hydrogen index (HI). They had both terrigenous and aquatic organic matter inputs. The kerogen was type II to III. They could produce both oil and gas during maturation. The Eocene source rocks were widely distributed in the Baiyun Depression. They had a huge thickness and high organic matter abundance. The organic matter had enough maturity to generate hydrocarbon from 18.5 Ma to the present. Therefore, the Eocene source rocks can provide sufficient hydrocarbon resources for deep-water petroleum accumulations and gas hydrate formations in the deep-water area of the PRMB.



Hydrate occupancy, morphology and spatial distribution in sediment pore can significantly affect the physical properties of hydrate-bearing sediment, but their evolutions with hydrate dissociation under various brine saturations are not well understood. X-ray micro-CT is employed to image the pore-scale dynamic process of methane hydrate dissociation in both sediments with different brine saturations. On the basis of processing and statistical analysis of X-ray CT images, several topological parameters, including volume, shape factor, fractal dimension and Euler characteristic of individual hydrate cluster, are selected to quantify hydrate occupancy, morphology and microstructure evolution with hydrate dissociation in the host sediments. Results show that the degree of brine saturation within the sediments can exert a significant impact on hydrate pore occupancy, morphology and microstructure connectedness during hydrate dissociation. In contrary to those of fully brine-saturated sediment, the topological parameters of individual hydrate cluster usually experience more dramatic changes with hydrate dissociation in partially brine-saturated sediment. It is inferred that in partially brine-saturated sediment the isolated hydrate clusters occupying in pore bodies are dissociated earlier in the initial experimental stage, and the dissociation of interpore hydrate frameworks interconnected through pore throats get dominated when hydrate saturation declines below a critical threshold value. On the other hand, in fully brine-saturated sediment the kinetics of pore-scale hydrate dissociation exhibit a completely opposite trend.

Wang, G., Li, Y., Wang, J., Jia, Z., Zhou, Y., Zhou, S., Xie, X., 2020. A modified receptor model for historical source apportionment of polycyclic aromatic hydrocarbons in sediment. Science of The Total Environment 702, 134931.


Pollution of polycyclic aromatic hydrocarbons (PAHs) in the environment is becoming increasingly serious with the development of the economy. Source analysis is the key step in reducing PAHs pollution in the environment, and existing methods are usually based on receptor models. However, when these methods are applied to the distribution of PAHs in sediments, overestimation or underestimation often occurs. Therefore, this paper proposes an improved model based on principal component analysis and multiple linear regression. The model has been applied to study the pollution of PAHs in sediments of Taihu Lake in China over several decades. Compared with existing models, principal component analysis followed by multiple linear regression of source (PCA-MLRS) can identify specific emission sources and quantify the impact of each emission, and the source resolution accuracy of the strong toxic molecules BaP and DBA is significantly higher than that of other models. Biomass combustion source is the main material source of Phe, Ant, Flu and Pyr in Taihu Lake sediment, and their contribution rates are 85.2%, 44.8%, 58.9% and 62.2%, respectively. The coal combustion source is the main material source of the 5-ring molecule BaP and the 6-ring molecules InP and BP. The contribution rates of coal combustion to BaP, InP and BP are 70.1%, 72.9% and 72.1%, respectively, and this contribution has increased since 1985. The contribution of petroleum oil combustion source and coal combustion source to PAHs in sediments of Taihu Lake is consistent. They are the main sources of heavy molecular PAHs such as BaA, BbF, BkF and DBA, and their contributions are 56.5%, 36.8%, 43.9% and 67.3% respectively. The results are related to the different emission and management characteristics of PAHs from different sources and the different behavior characteristics of low and high molecular weight PAHs in the environment.



Dissolved organic matter (DOM) is a critical component of high-strength organic wastewater, and the study of them from molecular perspective could improve the removal efficiency. Leachate samples were collected from China’s largest two stage anaerobic/aerobic membrane bioreactor and nanofiltration (A/O-MBR-NF) process, with the treatment capacity of 5000 t/d, and characterized by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) from molecular perspective. High molecular weight (m/z > 500) compounds with 40–50 carbon atoms and 15–20 double bond equivalence (DBE) were biodegraded into medium molecular weight compounds with 10–20 carbon atoms and ∼10 DBE. Contribution of lipids and unsaturated hydrocarbons compounds in DOM turned into 42.1% and 2.5%, respectively, while contribution of condensed aromatics in DOM dramatically increased to 15.4% in leachates along the A/O-MBR process. Most of DOM was converted into higher polymerization degree and accumulated in concentrated leachate (CL). Sulfur-containing compounds, whose relative peak ratio accounted for 56.4%, were regarded as recalcitrant DOM in CL. Increase of retention time in anaerobic unit for raw leachate might be useful for decomposing the long-chain organic compounds, which could also reduce loadings for the following A/O-MBR process. Well-focus techniques such as sulfur-oxidation bacteria could be introduced into the MBR unit for better removing organo-sulfur compounds. Advanced oxidation processes for CL degradation would be efficiency for the removal of recalcitrant DOM. Thus, leachate could be disposed in a zero-discharge way based on the practical experience of such a typical working treatment process.

Wang, H., Li, Z., Zhuang, W.-E., Hur, J., Yang, L., Wang, Y., 2020. Spectral and isotopic characteristics of particulate organic matter in a subtropical estuary under the influences of human disturbance. Journal of Marine Systems 203, 103264.


Particulate organic matter (POM) in the coastal zone plays an important role in global carbon cycle, yet its spectral properties under human disturbance are not well understood. This study investigated the source and dynamics of POM in a typical coastal area (Minjiang Estuary, China) under the influences of estuarine mixing, urbanization and dam construction, based on spectral and isotopic analysis. The yield of particulate organic carbon from the watershed (0.38 g m−2 yr−1) was in part limited by the historical decrease in sediment discharge downstream hydropower station. The absorption and fluorescence indices of POM suggested an important contribution from biological production with a low humic content. The importance of river and estuarine production was supported by elemental and isotopic analysis, in particular for N-bound constituents of POM. Three humic-like and two protein-like fluorescent components were identified from POM using fluorescence excitation-emission matrices-parallel factor analysis (EEMs-PARAFAC). They showed weak correlations with salinity, suggesting non-conservative behaviors of fluorescent POM during the estuarine mixing. Principal component analysis (PCA) identified two principal factors, which were related to the level of chromophoric POM (PC1) and biological production (PC2), respectively. The PCA results indicated stronger influence of biological production in the estuarine zone and potential effect of sediment re-suspension and/or wastewater discharge in the urban zone. Overall, our results demonstrated significant influences of human disturbance on the flux, source and dynamics of POM in the coastal zone, which could be assessed by spectral and stable isotopic analysis.

Wang, J., Han, X., 2019. Analytical challenges of shotgun lipidomics at different resolution of measurements. TrAC Trends in Analytical Chemistry 121, 115697.


The essence of shotgun lipidomics is to maintain consistency of the chemical environment of lipid samples during mass spectrometry acquisition. This strategy is suitable for large-scale quantitative analysis. This strategy also allows sufficient time to collect data to improve the signal-to-noise ratio. The initial approach of shotgun lipidomics was the electrospray ionization (ESI)-based direct infusion mass spectrometry strategy. With development of mass spectrometry for small molecules, shotgun lipidomics methods have been extended to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and ambient mass spectrometry, including MS imaging methods. Furthermore, the object of analysis has extended from organ and body fluid levels to tissue and cell levels with technological developments. In this article, we summarize the status and technical challenges of shotgun lipidomics at different resolution of measurements from the mass spectrometry perspective.

Wang, L., Liu, H., Chen, S., Wang, M., Liu, Y., Yu, W., Zhang, X., 2019. Crude oil-contaminated soil treatment and oil recovery through micro-emulsion washing. Energy & Fuels 33, 11486-11493.


Removal of crude oil from oil-contaminated soil using a micro-emulsion (ME) washing method was carried out in this work. The influence of the oil/water ratio on the phase behavior of the ME was studied by the phase diagram. As the oil/water ratio (Vo/Vw) increased, Winsor type I ME presented and the phase state of the system remained unchanged. Comparison between the original and the recovered crude oil and soil samples was done. It is found that the ME treatment has little influence on the physical and chemical properties of the soil. The recovered crude oil has higher saturation fraction, lower aromatic, resin, and asphaltene content, and lower density and viscosity and belongs to light crude oil. Experiments on effects of diesel oil amount, temperature, reusing times, and scaling-up were carried out using the selected three types of ME formulation. The optimal ME formulation for the de-oiling of crude oil contaminated soil is w(SDBS) = 10%, w(n-butanol) = 4.8%, w(NaCl) = 0.8%, and w(diesel) = 13.6%. The most suitable temperature for treating oily soil by ME is 35–50 °C, and the treating effect is still stable when the capacity is scaled up by 6000 times.

Wang, N., Li, M., Liu, X., Hong, H., Tian, X., Yang, C., Shi, S., Liu, P., 2020. Geo-chromatographic fractionation effect of methyldibenzofuran in dolomite reservoirs and its application in tracing oil filling pathways in the Sichuan Basin. Marine and Petroleum Geology 113, 104126.


Dibenzofuran and its methyl substituted homologues are the important oxygen-containing polycyclic aromatic compounds in crude oils. The ratio of 1-/4-methyldibenzofuran has been successfully used in sandstone reservoir tracing oil migration orientation. Here we focus on the geo-chromatographic fractionation effect of methyldibenzofuran (MDBF) in dolomite reservoirs. We calculated the charge density differences between 1-methyldibenzofuran (1-MDBF) and 4-methyldibenzofuran (4-MDBF) based on density functional theory. The EIn between MDBF isomers and dolomite (104) surface was also calculated according to molecular dynamics simulation. The result show that comparing with the 4-MDBF, there is strong interaction between 1-MDBF and dolomite (104) surface leading the ratio of 1-MDBF and 4-MDBF increase with the migration distance. There is no significant correlation between bitumen reflectance and the ratio of 1-MDBF and 4-MDBF in our samples. In addition, molecular simulation results show that the MDBF isomers are thermodynamically stable and dissociation of Ph-CH3 is difficult to occur under geological condition. All these demonstrate that 1-MDBF and 4-MDBF can be survived after oil-cracking to gas and pyrobitumen. Therefore, in theory, the ratio of 1-/4-methyldibenzofuran is also regarded as an index for oil migration orientation in dolomite reservoir. Gas chromatography-mass spectrometry results show that MDBFs occur at relatively higher abundance in the bitumens of the Ediacaran Dengying Formation (Z2dn4) and Cambrian Longwangmiao Formation (Є1l) in the Sichuan Basin. The ratio of 1-/4-methyldibenzofuran has been successfully used to trace the crude oil filling pathway in the Z2dn4 and Є1l dolomite reservoir in the Sichuan Basin in this study. Two preferential filling orientations (i.e. from west to east and from north to south) for paleo-oil have been identified in the contour maps of 1-/4-methyldibenzofuran in the Z2dn4 and Є1l, which is consistent with the geological background.

Wang, P., Algeo, T.J., Zhou, Q., Yu, W., Du, Y., Qin, Y., Xu, Y., Yuan, L., Pan, W., 2019. Large accumulations of 34S-enriched pyrite in a low-sulfate marine basin: The Sturtian Nanhua Basin, South China. Precambrian Research 335, 105504.


The Cryogenian of the Nanhua Basin (eastern Guizhou Province, South China) consists of a continuous succession of glacial and post-glacial deposits from the Sturtian Glaciation, including diamictite of the Tiesi’ao Formation and Mn-carbonate and black shale of the overlying lower Datangpo Formation. Here, we analyzed the sulfur chemistry of these units with the goal of understanding regional to global changes in the marine sulfur cycle accompanying a Snowball Earth event. The study units are characterized by elevated carbonate-associated sulfate (CAS) δ34S (mean +56.0‰, range +49.6 to +62.6‰) and pyrite δ34S compositions (mean +57.5‰, range +48.8 to +66.8‰). Both CAS and pyrite δ34S show water-depth gradients, with mean values increasing from the shallower Lijiawan area (CAS: +49.3‰; pyrite: +44.5‰) to the deeper Xixibao (CAS: +57.9‰; pyrite: +59.8‰) and Gaodi areas (CAS: +62.4‰; pyrite: +61.6‰), reflecting a density-stratified water column with limited vertical mixing. △34S values (i.e., δ34SCAS – δ34Spy) range from −6.5‰ to +8.0‰ with a mean of +0.7‰. These features, which are similar to those for coeval strata globally, are consistent with low seawater sulfate concentrations, but several additional features of the Nanhua Basin deposits do not conform to existing Cryogenian sulfur-cycle models: (1) high total sulfur contents (mean 2.2 ± 1.1%), which are difficult to reconcile with low seawater sulfate, and (2) frequent negative △34S values, which indicate that in situ microbial sulfate reduction (MSR) cannot have been the sole control on pyrite δ34S. These features point to quantitatively important hydrothermal sulfur inputs to the Nanhua Basin watermass. Based on these considerations, we propose a new sulfur-cycle model for the Sturtian Nanhua Basin in which hydrothermal emissions supplied large amounts of 34S-enriched H2S to the water column. The released H2S was partly precipitated as syngenetic framboidal pyrite and partly oxidized to sulfate that was removed to the sediment as CAS, thus accounting for the unusual combination of high total sulfur concentrations, similar strongly 34S-enriched sulfur-isotopic compositions for CAS and pyrite, and frequent negative △34S values. As a result of low seawater sulfate

concentrations, both δ34SCAS and δ34Spy developed water-depth gradients through vertical mixing of strongly 34S-enriched hydrothermal sulfide from deep-graben vents with moderately 34S-enriched sulfate from the global ocean. Our model provides new insights into Sturtian-glacial sulfur cycling processes within a semi-restricted marine basin that are likely to have wider applicability to Neoproterozoic marine systems.

Wang, R., Shen, B., 2019. Snowball Earth at low solar luminosity prevented by the ocean–atmosphere coupling. Acta Geochimica 38, 775-784.

https://doi.org/10.1007/s11631-019-00373-7

The standard solar model proposes that the solar luminosity was 30% lower than the present level at 4.5 billion years ago (Ga). At low solar radiation, the climate model predicts that the Earth should have been completely covered by ice in the first 2 billion years, i.e. in the snowball Earth climate mode, when the atmospheric CO2 content was at the present level. However, snowball Earth condition is inconsistent with various sedimentological, paleontological, and geochemical evidence. Such controversy is collectively known as the ‘Faint Young Sun’ (FYS) paradox. Though various models have been proposed, the FYS paradox has not yet been resolved. In this study, we develop a model by considering the ocean–atmosphere coupling to show that high atmospheric CO2 level could be sustained at low seawater pH. The modeling result indicates that 0.1 bar atmospheric CO2 level that was required to prevent snowball Earth in early Archean could be sustained at seawater pH of 6.8–7.2. Although the absence of siderite in Archean paleosols has been used to argue against high atmospheric CO2 level, we suggest that siderite precipitation in paleosols was not controlled by the atmospheric CO2 level alone. Instead, siderite could precipitate in anoxic conditions with various amount of CO2 in the atmosphere, suggesting siderite cannot be used to reconstruct the atmospheric CO2 level. Therefore, the new model suggests that the snowball Earth condition could be prevented by the coupling of atmosphere and ocean systems, and thus the emergence of the ocean in the very beginning of Earth evolution might be the key to the subsequence evolution of habitability.

Wang, X., Liu, L., Wang, Y., Sheng, Y., Zheng, S., Luo, Z., 2019. Control of lithofacies on pore space of shale from Longmaxi Formation, southern Sichuan Basin. Acta Petrolei Sinica 40, 1192-1201 http://www.syxb-cps.com.cn/EN/abstract/abstract5765.shtml

The pore types of shale, quantitative characterization of pore structures and control factors of pore spaces are important topics in research of shale reservoir. The shale lithofacies of Longmaxi Formation in the southern Sichuan Basin can be classified into siliceous shale, mixed shale and argillaceous shale according to the mineral composition. The pore types, structural characteristics and control factors of pore spaces of different shale lithofacies of Longmaxi Formation in the southern Sichuan Basin were analyzed by technologies of quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN), low temperature N2 and CO2 adsorption and high pressure mercury intrusion experiments. The results show that the argillaceous shale is mostly characterized by the sheet-like intragranular pores of clay minerals and filled with the migrated organic matters; the mixed shale is rich in organic matter pores and carbonate dissolved macropores; siliceous shale is rich in organic matter pores. The total surface porosities of shale is mainly provided by the pores with the diameter of 0-500 nm. The surface porosity of minerals (except carbonate and feldspar)and organic matters are mainly contributed by intragranular pores. The surface porosity of organic matter is up to 32.37%, 8 to 16 times higher than that of mineral particles. The mesopores of shale are the main contributors to the pore volume, while micropores make a major contribution to the specific surface area of pores. The average surface porosity, pore volume and pore specific surface area of mixed shale are similar to those of siliceous shale, which means the mixed shale has potential storage capacity. The pore space of mixed shale and siliceous shale with high TOC content is mainly controlled by organic matter pores, but the pore space of argillaceous shale with lower TOC content is mainly controlled by organic matter pores and illite mineral related pores.

Wang, X.W., F Fu2, Pingping Qu2, Kling2, Jiang3, Y Gao1,4, and David A. Hutchins2 , Fu, F., Qu, P., Kling, J.D., Jiang, H., Gao, Y., Hutchins, D.A., 2019. How will the key marine calcifier Emiliania huxleyi respond to a warmer and more thermally variable ocean? Biogeosciences 16, 4393-4409.


Global warming will be combined with predicted increases in thermal variability in the future surface ocean, but how temperature dynamics will affect phytoplankton biology and biogeochemistry is largely unknown. Here, we examine the responses of the globally important marine coccolithophore Emiliania huxleyi to thermal variations at two frequencies (1 d and 2 d) at low (18.5 ∘C) and high (25.5 ∘C) mean temperatures. Elevated temperature and thermal variation decreased growth, calcification and physiological rates, both individually and interactively. The 1 d thermal variation frequencies were less inhibitory than 2 d variations under high temperatures, indicating that high-frequency thermal fluctuations may reduce heat-induced mortality and mitigate some impacts of extreme high-temperature events. Cellular elemental composition and calcification was significantly affected by both thermal variation treatments relative to each other and to the constant temperature controls. The negative effects of thermal variation on E. huxleyi growth rate and physiology are especially pronounced at high temperatures. These responses of the key marine calcifier E. huxleyi to warmer, more variable temperature regimes have potentially large implications for ocean productivity and marine biogeochemical cycles under a future changing climate.

Wang, Y.-f., Zhai, G.-y., Lu, Y.-c., Ma, Y.-q., Li, J., Liu, G.-h., Zhang, Y.-x., 2019. Sedimentary lithofacies characteristics and sweet-spot interval characterization of the Sinian Doushantuo Formation in Upper Yangtze Platform, South China. China Geology 2, 261-275.


ABSTRACT The Sinian Doushantuo Formation is the oldest shale gas reservoir discovered in the world, which contains good shale gas shows as the Eyangye-1 and Zidi-1 wells in the Yichang Region of western Hubei province, China. The shales in the Doushantuo Formation feature considerable thickness (135 m), high gas content (4.83 m3/t) and high fragile mineral content (up to 75%). Due to the influences of the sedimentary environment, the shale reservoirs here have high dolomitic content (54%) and abruptly changes in vertical lithofacies. Moreover, the characteristics of the shale sweet-spot differ significantly from that in the Wufeng Formation and Longmaxi Formation in southeast Sichuan Basin. A high-resolution sequence stratigraphic correlation was performed on the shales of the Doushantuo Formation at the Eyangye-1 well, Zidi-1 well, Zidi-2 well and some outcrop profiles in Yichang area for the identification of their sedimentary microfacies characteristics. A comprehensive comparative analysis was made by incorporating the elemental geochemistry, wireline and mud logging data of the well to further identify the sweet-spot interval therein. With the analysis of Eyangye-1 well, the sweet-spot interval of the Doushantuo Formation is 3360−3408 m, of which sedimentary microfacies is deepwater reduced environment with many pyrite laminaes, and the TOC is high to 3.42%, the Ro is 3.3%, the organic and matrix pore are well developed and the aperture more than 50 nm, the porosity is 2.7%, the desorption gas content average is 2.16%, and the main mineral is dolomitic (54%) and siliceous quartz (21%). Additionally, these parameters combined with previous studies will shed light on evaluating and characterizing the layers therein, also provide referential geological data for the following exploration and development activities of this shale system.

Wang, Y.-Y., Wang, X.-Q., Hu, B., Luo, M., 2019. Tomographic reconstructions of crab burrows from deltaic tidal flat: Contribution to palaeoecology of decapod trace fossils in coastal settings. Palaeoworld 28, 514-524.


Trace fossils play an important role in reconstructing palaeoecology and depositional environment. Their palaeoecological implications can be better understood when the trace makers are correctly identified. Neoichnology studies the burrow morphologies, behavioral ecology of modern organisms and their interaction with the environment. Neoichnology is of great significance in linking burrowing behaviors of extant organisms with interpretation of trace fossil palaeoecology. This paper reports a study on burrows produced by the ocypodid crab (Macrophthalmus japonicus De Haan) in the tidal region of the Yellow River Delta using CT scanning techniques. Our results show that M. japonicus produces abundant I-, U-, and Y-shaped burrows in a mudflat of the delta. These domicile structures are similar in morphological characteristics to the trace fossil

Psilonichnus, suggesting M. japonicus as its possible additional trace maker. Our study supports the usage of Psilonichnus as a significant palaeoenvironmental indicator for coastal and shelf environments. Furthermore, this study highlights the great potential of applying CT techniques in future ichnological-related studies.



The Chang 6, Chang 8, and Chang 9 reservoirs of the Upper Triassic Yanchang Formation in the Zhenjing area of the Ordos Basin are characterized by low porosity, low permeability, high oil saturation, and large oil reserves, which indicate huge tight oil potential. To comprehensively investigate the hydrocarbon contributors and charging history, fluid inclusions were systemically studied coupled with basin modeling and oil geochemical analysis. According to the petrographic characteristics, two episodes of fluid inclusions occurred in each of the three reservoirs. Microthermometry analysis suggests that the hydrocarbon inclusions of the first episode in each reservoir are distributed mainly along overgrowth quartz or secondary microcracks and exhibit light yellow or light brown fluorescence; the coeval aqueous inclusions display low homogenization temperature (Th) peaks with 80–100 °C. The hydrocarbon inclusions of the second episode in each reservoir are mainly distributed in microcracks that cut across or within quartz grains and exhibit light green or bluish-green fluorescence; the coeval aqueous inclusions are characterized by high Th peaks with 110–120 °C. The different characteristics of the two episodes of the fluid inclusions imply the existence of two episodes of hydrocarbon charging events. The burial and geothermal histories of the various reservoirs were reconstructed using one-dimensional basin modeling and pressure–volume–temperature–composition (PVTX) simulation coupled with the authigenic illite K–Ar dating. The reconstruction implied the time of the two hydrocarbon charging episodes to be Early Cretaceous and Late Cretaceous. Oil-source correlation studies illustrate that the Chang 6, Chang 8, and Chang 9 crude oils all originate from the Chang 7 source rock. The migration characteristics and directions were comprehensively analyzed by using maturity parameters. This explanation of the charging history and oil migration pathway of the Upper Triassic Yanchang Formation in the Zhenjing area provides a theoretical basis for further exploration.

Wang, Y., Liu, Y., He, J., Zhang, Y., 2019. Redox-neutral photocatalytic strategy for selective C–C bond cleavage of lignin and lignin models via PCET process. Science Bulletin 64, 1658-1666.


It remains challenging to achieve the selective cleavage of C–C bonds in lignin or lignin model compounds to produce aromatic products in high yield and selectivity. We have developed a redox-neutral photocatalytic strategy to accomplish this goal in both β-O-4 and β-1 lignin models at room temperature (RT) via proton-coupled electron transfer (PCET) process without any pretreatments of substrate, by adjusting the alkalinity of base to obtain a lignin models/base PCET pair with a bond dissociation free energy close to 102 kcal/mol. Without breaking down Cβ–Cγ bond and any C–O bonds, this PCET method is 100% atom economy and produces exclusive Cα–Cβ bond cleavage products, such as benzaldehydes (up to 97%) and phenyl ethers (up to 96%), in high to excellent yields and selectivities. Preliminary studies indicated that the PCET strategy is also effective for the depolymerization of native lignin at RT, thus providing significantly important foundation to the depolymerization of lignin.

Wang, Y., Zhu, Y., Zhang, R., Anovitz, L.M., Bleuel, M., Liu, S., Chen, S., 2020. SANS coupled with fluid invasion approaches for characterization of overall nanopore structure and mesopore connectivity of organic-rich marine shales in China. International Journal of Coal Geology 217, 103343.


The pore structure of shales, including pore morphology, connectivity, pore volume, specific surface area (SSA), and pore size distribution (PSD), is a significant factor in controlling gas storage and transport and the migration mechanisms of hydrocarbons. However, the lack of comprehensive characterization for both accessible and inaccessible pore structure increases the difficulty of gas-in-place estimation and gas exploration. In order to investigate the nanoscale pore system, integration of high-pressure mercury intrusion porosimetry (MIP), low-pressure N2/CO2 adsorption (LNA/LCA), and small-angle neutron scattering (SANS) were employed to obtain a multi-scale quantitative characterization of the nanopore structure of organic-rich marine shale samples from the Longmaxi and Niutitang Formations in China. PSDs obtained from the combined techniques appropriately cover an overall nanopore size range of shale (0.35–15,000 nm) and overcome the limits of the individual method. Uni-, bi, and multi-modal PSDs were observed, but the sizes of a significant portion of the nanopores observed in these shales range from 0.35 to 100 nm. Pore volumes and surface areas of micropores (<2 nm), mesopores (2–50 nm), and macropores (>50 nm) were characterized based on the best performance window of each technique: LCA for micropores; LNA and SANS for mesopores; and MIP for macropores. It was found that micropores are the major contributor to the total SSA for both the Longmaxi and Niutitang shales. With respect to pore volume, however, the contribution to the total pore volume has a trend of micropore < mesopore < macropore for the Longmaxi shale samples, but micro-/mesopore volumes are greater than macropore volumes for samples of the Niutitang shale. Strong correlations were also observed between total organic carbon (TOC) content and micropore volume and surface area, which implies that organic matter is a controlling factor in the micropore system of organic-rich shales. In addition, strong correlations between methane adsorption capacity and both micro-/mesopore volumes and SSAs indicate that micro-/mesopores are governing factors for methane storage. Furthermore, the fractions of accessible mesopore volume and surface area were quantitatively estimated by SANS and LNA. Correlation analyses suggest that the accessibility of the mesopore surface area could be an indicator for gas transport and storage in mesopores in organic matter. Thus, a shale with higher connectivity could have higher gas diffusion capability but lower gas adsorption capacity, and vice versa.

Wanner, P., Hunkeler, D., 2019. Molecular dynamic simulations of carbon and chlorine isotopologue fractionation of chlorohydrocarbons during diffusion in liquid water. Environmental Science & Technology Letters 6, 681-685.

https://doi.org/10.1021/acs.estlett.9b00640

Until now, the magnitude of isotopologue fractionation of organic compounds due to aqueous-phase diffusion has been quantified only experimentally. This study aims to determine the extent of aqueous-phase diffusion-induced isotopologue fractionation of organic compounds for the first time on a computational basis using molecular dynamic simulations (MDS). The MDS were conducted for different organic compounds including chlorinated ethenes (trichloroethene (TCE)) and ethanes (1,2-dichloroethane (1,2-DCA)) and for different isotopologues (carbon and chlorine). The MDS revealed a weak power law mass (m) dependency of the diffusion coefficient (D ∝ m–β with β ≤ 0.049) for carbon and chlorine isotopologues of TCE and 1,2-DCA, consistent with experimental results. The MDS showed that the mass of the diffusing species is the key controlling factor for diffusion-induced isotopologue fractionation and not the molecular volume as suggested by previous studies. Furthermore, the MDS revealed that the weak power law mass dependency of the diffusive transport rate originates from an interplay between strongly mass-dependent short-term and mass-independent long-term solute–solvent interactions. Hence, the presented MDS results provide for the first a time a theoretical rationale for the experimentally observed magnitude of isotopologue fractionation of organic compounds caused by aqueous-phase diffusion.

Warr, O., Giunta, T., Ballentine, C.J., Sherwood Lollar, B., 2019. Mechanisms and rates of 4He, 40Ar, and H2 production and accumulation in fracture fluids in Precambrian Shield environments. Chemical Geology 530, 119322.


Fluids residing in fractures in Precambrian Shield environments can contain gases with concentrations up to 30% 4He, 6% 40Ar, and more than 50% H2 depending on the location (expressed as % volume of the free gas phase post-exsolution). These gases are produced through two distinct mechanisms; 1. Radioactive decay of naturally occurring U, Th, and K which produces H2 via radiolysis of water and the noble gases (e.g. 4He and 40Ar) and, 2. Hydration reactions with mafic and ultramafic minerals in the host rock that produce H2. He production is economically important as known reservoirs of 4He and 3He, resources integral to medical applications and different manufacturing sectors, are rapidly depleting. H2 meanwhile has recently been posited as an emerging, clean, energy source for a post-hydrocarbon energy future. 40Ar, though more common, also has important applications in research and industry. The accumulation of 4He and 40Ar can also be used to provide vital constraints on fluid residence times, crucial to understanding planetary processes. In both planetary science and astrobiology there is also keen interest in H2 as an energy source supporting subsurface microbial metabolisms and/or abiotic organic synthesis. For both H2 and 4He, innovative exploration strategies are required to understand their production and accumulation in the deep crust. At present few studies have specifically focussed on establishing the relationship between these two reactive and conservative elements in the deep subsurface, despite their cogenetic nature.

We investigate the dependence of H2, 4He, and 40Ar production rates on rock type and geologic setting. Through collating and combining previously published dissolved gas data with substantial new data for specific localities, conservative estimates of H2 production are generated for a range of sites across the Canadian Shield. The results support the prevailing theory that H2 production dominantly depends on the associated lithology. This study also identifies broadly homogeneous 4He and 40Ar production rates based on a relatively homogeneous range of U, Th, and K concentrations in the source rocks. As a consequence, H2/4He ratios are relatively low in felsic environments where H2 is mostly produced radiolytically, whereas they are elevated in mafic environments due to additional H2 production through hydration reactions (e.g. serpentinization). Extrapolating to Precambrian terrains globally this study estimates the total annual production of 4He and 40Ar from these environments specifically to the worldwide budget and reports here a global production in these environments comparable to both production in the entire oceanic crust and to the total net outgassing of these elements at Mid-Ocean Ridges.

Warren, J.L.A., Ponce de León, M.S., Hopkins, W.D., Zollikofer, C.P.E., 2019. Evidence for independent brain and neurocranial reorganization during hominin evolution. Proceedings of the National Academy of Sciences 116, 22115-22121.


Significance: Human brains differ substantially from those of great apes, and equally important differences exist between their braincases. However, it remains unclear to which extent evolutionary changes in brain structure are related to changes in braincase structure. To study this question, we use combined computed tomography (CT) and MRI head data of humans and chimpanzees and quantify the spatial correlations between brain sulci and cranial sutures. We show that the human brain–braincase relationships are unique compared to chimpanzees and other great apes and that structural rearrangements in the brain and in the braincase emerged independently during human evolution. These data serve as an important frame of reference to identify and quantify evolutionary changes in brain and braincase structures in fossil hominin endocasts.

Abstract: Throughout hominin evolution, the brain of our ancestors underwent a 3-fold increase in size and substantial structural reorganization. However, inferring brain reorganization from fossil hominin neurocrania (=braincases) remains a challenge, above all because comparative data relating brain to neurocranial structures in living humans and great apes are still scarce. Here we use MRI and same-subject spatially aligned computed tomography (CT) and MRI data of humans and chimpanzees to quantify the spatial relationships between these structures, both within and across species. Results indicate that evolutionary changes in brain and neurocranial structures are largely independent of each other. The brains of humans compared to chimpanzees exhibit a characteristic posterior shift of the inferior pre- and postcentral gyri, indicative of reorganization of the frontal opercular region. Changes in human neurocranial structure do not reflect cortical reorganization. Rather, they reflect constraints related to increased encephalization and obligate bipedalism, resulting in relative enlargement of the parietal bones and anterior displacement of the cerebellar fossa. This implies that the relative position and

size of neurocranial bones, as well as overall endocranial shape (e.g., globularity), should not be used to make inferences about evolutionary changes in the relative size or reorganization of adjacent cortical regions of fossil hominins.



Due to increased sea transport and offshore gas and oil exploration, the Arctic is facing an unprecedented risk of marine oil spills. Although beached oil spills can lead to acute and chronic impacts on intertidal ecosystems, the effects of oil spills on macro-algae in Arctic ecosystems is lacking. Here, we assessed the effect and response of the tidal macro-algae Fucus distichus to oiling, i.e. self-cleaning potential by seawater wash and photosynthetic activity. Oiling with four oil types (ANS, Grane, IFO30 and MGO) was simulated by exposing F. distichus tips to oil. Oil removal half-times ranged between 0.8 - 4.5 days, indicating that oiling of macro-algae with the tested oils was short-term. Further, Grane oil mostly inhibited photosynthetic activity whereas oil from ANS, IFO30 and MGO stimulated it. The photosynthetic activity of F. distichus continued to be affected (inhibited or stimulated), even after oil on the tip surface was washed off.

Wei, H., Tang, Z., Yan, D., Wang, J., Roberts, A.P., 2019. Guadalupian (Middle Permian) ocean redox evolution in South China and its implications for mass extinction. Chemical Geology 530, 119318.


The Guadalupian mass extinction was a long-term biocrisis that started in the early Guadalupian Epoch (Permian Period). Many studies of the causes of the extinction have focused on the late Guadalupian, although the entire Guadalupian should be studied to address its origins. The selective nature of the species removed during the Guadalupian extinction also remains a puzzle. Here, we present pyrite framboid size distributions, pyrite-sulfur isotopic compositions, and C-N-S profiles for the entire Guadalupian from South China to develop a record of ocean redox evolution to help understand the selective extinction. Our results indicate that euxinia was mostly persistent in the deep-water platform basin throughout the Guadalupian, which triggered long-term Early and Middle Guadalupian shallow-water dysoxia and frequent episodic Late Guadalupian euxinia events that resulted in a gradual long-term Early and Middle Guadalupian diversity decrease and selective Late Guadalupian extinction. The combined effect of euxinia and global regression led to selective extinction of taxa that had weakly buffered respiratory physiology and high growth efficiency, such as brachiopods, large fusulinids, and giant bivalves.

Wei, J., Li, J., Zhou, X., Zhang, X., 2020. Effect of pressure and CO2 content on the asphaltene precipitation in the light crude oil. Petroleum Science and Technology 38, 116-123.

https://doi.org/10.1080/10916466.2019.1684947

This paper focus on the effect of the pressure and CO2 content on the state of asphaltene in the light crude oil from Changqing oilfield. When the pressure is more than 7 MPa or the CO2 content is more than 10%, the aggregation of the asphaltene occurs. With the increase of the pressure from 7 MPa to 10 MPa or the increase of CO2 content from 10% to 40%, the amount of the asphaltene aggregates has a significant increase. The experiment results of the effect of CO2 content and pressure on the asphaltene precipitation in the light crude oil is different from that of the heavy oil. The conclusion can provide a theoretical basis to avoid the asphaltene precipitation the light crude oil during CO2 flooding.

Wei, S., Liu, Y., Kou, X., Huang, S., Chen, G., Xu, L., Tong, Q., Zhu, F., Xu, J., Ouyang, G., 2019. Energy-efficient construction of thermally stable superhydrophobic nanoscale stacked lamellae based solid-phase microextraction coating for the determination of non-polar compounds. Analytica Chimica Acta 1092, 17-23.


Herein, through a facile and energy-friendly approach, thermally stable manganese-derived amorphous stacked nanosheet (MASNS) coatings with controlled wetting property ranging from superhydrophilicity to superhydrophobicity were synthesized. The superhydrophobic MASNS coating exhibited remarkable selectivity and sensitivity in the solid phase microextraction (SPME) of non-polar aromatic analytes, even amid the abundance of polar compounds, due to the superhydrophobic effect and the stacked lamellar structures. The established method was applied to the determination of polycyclic aromatic hydrocarbons (PAHs), featuring low LODs (i.e., 0.14–0.24 ng L−1) and wide linear ranges (e.g., 10–10000 ng L−1). Extraction and desorption conditions were optimized to unleash the potential of the fiber before it was applied to the analysis of target analytes in real water samples, where satisfactory recoveries were obtained (81.7%–114.2%). This work might provide critical insights for the scalable production of superhydrophobic nanosheets as affordable and high-performance adsorbents.

Wei, Y., Chen, G., Lu, S., Song, Z., Qi, R., Wang, W., Gong, D., Wang, F., 2019. Re-examination of genetic types and origins of natural gases from Dibei bulge, eastern Luliang uplift, Junggar Basin, China. Journal of Natural Gas Geoscience 4, 257-265.


The eastern part of Luliang uplift has currently become the main target for gas exploration in the Junggar Basin. By now, several giant–medium gas fields (reservoirs) are discovered in the Dinan bulge. Located north to the Dinan bulge, the Dibei bulge is surrounded by several hydrocarbon generating sags and developed several sets of source rocks, which promises a favorable gas accumulation condition. Based on molecular and stable carbon isotopic compositions of nine gas samples from the Dibei bulge, in cooperation with the burial and hydrocarbon generation history of source rocks, genetic types and origins of natural gases and related secondary alterations were fully discussed in this study. A comparative study was also carried out with the geochemical characteristics of natural gases from the Dinan bulge. Gases from the Dibei bulge have complicated origins which could primarily be divided into three types: (1) highly-mature coal-derived gas generated from the Upper Carboniferous Batamayineishan coal measures; (2) highly-mature oil-type gas generated from the marine source rocks in the Lower Carboniferous Jiangbasitao Formation or Songkaersu Formation; (3) secondary microbial methane generated via the biodegradation of oils. Significant differences have been observed between gases from the Dibei and Dinan bulges in the concentration of non-hydrocarbon gases, carbon isotopes and thermal maturities. Gases from the Dibei bulge are at highly mature stage, which correlates well with the maturities of Carboniferous source rocks in the Ulungu depression. Thus, these gases are most probably derived from the Ulungu Depression.

Weiner, I., Shahar, N., Marco, P., Yacoby, I., Tuller, T., 2019. Solving the riddle of the evolution of Shine-Dalgarno based translation in chloroplasts. Molecular Biology and Evolution 36, 2854-2860.


Chloroplasts originated from an ancient cyanobacterium and still harbor a bacterial-like genome. However, the centrality of Shine–Dalgarno ribosome binding, which predominantly regulates proteobacterial translation initiation, is significantly decreased in chloroplasts. As plastid ribosomal RNA anti-Shine–Dalgarno elements are similar to their bacterial counterparts, these sites alone cannot explain this decline. By computational simulation we show that upstream point mutations modulate the local structure of ribosomal RNA in chloroplasts, creating significantly tighter structures around the anti-Shine–Dalgarno locus, which in-turn reduce the probability of ribosome binding. To validate our model, we expressed two reporter genes (mCherry, hydrogenase) harboring a Shine–Dalgarno motif in the Chlamydomonas reinhardtii chloroplast. Coexpressing

them with a 16S ribosomal RNA, modified according to our model, significantly enhances mCherry and hydrogenase expression compared with coexpression with an endogenous 16S gene.

Wen, D., Ordonez, D., Valencia, A., McKenna, A.M., Chang, N.-B., 2020. Copper impact on enzymatic cascade and extracellular sequestration via distinctive pathways of nitrogen removal in green sorption media at varying stormwater field conditions. Chemosphere 243, 125399.


Nutrient removal efficiency in green sorption media such as biosorption activated media (BAM) for treating stormwater runoff can be heavily influenced either on a short- or long-term basis by varying field conditions of linear ditches due to the presence of copper in stormwater runoff. It is also noticeable that the linear ditch undergoes physical or mechanical impacts from the traffic compaction, chemical impact of carbon sources from the nearby farmland, and biological impact from potential animal activities (such as gopher tortoises, moles, and ants). In the nitrogen cycle, two denitrification pathways, the dissimilatory nitrate reduction to ammonia and common denitrification, are deemed critical for such assessment. A fixed-bed column study was set up to mimic different linear ditch field conditions for BAM applications and measure the effect of short-and long-term copper addition on microbial dynamics given the varying decomposition of dissolved organic nitrogen (DON). The findings confirm that, as the denitrifiers (in the second pathway) were the dominant species, their population continued to grow and maintain small-sized cells for extracellular sequestration under long-term copper impact. Furthermore, the study indicated that the ammonia oxidizer comammox was found in higher quantities than ammonia oxidizing bacteria or archaea. An enormous amount of DON was released during this process to bind the copper ion and reduce its toxicity as the enzymatic cascade effect appeared. In addition, the long-term copper exposure posed salient inhibitory effects on the microbial community regardless of varying field conditions in BAM. Short-term copper toxicity exerted an important but varying role in the enzymatic cascade effect over different linear ditch field conditions in BAM.

Wen, S., Liu, J., Deng, J., 2019. Fluid Inclusion Effect in Flotation of Sulfide Minerals. Elsevier. 246 pp.

https://doi.org/10.1016/C2019-0-00356-1

Fluid Inclusion Effect in the Flotation of Sulfide Minerals gives a detailed introduction to how fluid inclusions affect the flotation of sulfide minerals. The book introduces the various fluids found in geology, detailing the properties of fluid inclusions and how to identify and analyze their composition. It gives the common chemical compositions of fluid inclusions, investigates the release of fluid inclusions in sulfide materials and some gangues, and presents the concentrations and solution chemistry of the released ions. Finally, the book considers the absorption mechanism and the interaction of some typical metal ions from fluid inclusions on the surface of sulfide minerals.

Key Features

· Analyzes the properties of a surface when in contact with a fluid inclusion and how the fluid released affects mineral processing and extraction

· Determines the heavy metals released from fluid inclusions

· Offers a comprehensive picture on how fluid inclusions affect flotation from both macro and microscopic viewpoints

· Presents the absorption mechanism and interactions of some typical metal ions from fluid inclusions on the surface of sulfide minerals

Chapter 1 - Mineral fluid inclusions

This chapter introduces the definition of mineral fluid inclusions, the formation and mechanism of inclusions, and changes in fluid inclusion after fluid capture and discusses the inevitability and universality of fluid inclusions in minerals. It starts by directly giving the definition of mineral fluid inclusions from the perspective of geology. It then reveals the formation process and mechanism of inclusions, including the formation of defects in mineral crystals and their fluid capture in crystals. After that, the changes in fluid inclusion after formation, including the phase changes and a series of physical changes, are summarized. At the end of the chapter, a discussion based on the definition and formation mechanism of fluid inclusions is given to illustrate the inevitability and universality of fluid inclusions existing in minerals.

Chapter 2 - Classification of fluid inclusions

This chapter introduces the classification of inclusions, which is a basis for the recognition and study of inclusions. It starts by summarizing the classification methods of inclusions. It then gives a detailed description of the genetic classification of inclusions, including primary inclusions, pseudo-secondary inclusions, secondary inclusions, and metamorphosed inclusions. After that, we focus on another very important classification method of inclusions, i.e., physical phase state. According to this method, inclusions can be classified into fluid inclusions and magmatic inclusions. The fluid inclusions include pure liquid inclusions, pure gas inclusions, liquid inclusions, gas inclusions, daughter mineral inclusions, etc. The magmatic inclusions include crystalline melt inclusions, vitreous melt inclusions, and fluid melt inclusions.

Chapter 3 - Methods for the detection and composition study of fluid inclusions

This chapter introduces the existing methods for detection and chemical composition analysis of fluid inclusions. It starts by introducing general optical microscopy research on fluid inclusions, including preparation of inclusion sheets, identification of fluid inclusions in the sheets, morphology of fluid inclusions under the microscope, and the phase state of matter in fluid inclusions. It then gives an overview of the modern research techniques for identifying fluid inclusions, including ultraviolet light microscopy, infrared microscopy, scanning electron microscopy, and high-resolution X-ray computed tomography. After that, it introduces how to determine the salinity of fluid inclusions. At the end of the chapter, it introduces the main extraction and analysis methods of fluid inclusion components, including the issues to be aware of in composition analysis of inclusions and the analytical methods of the chemical composition of group inclusions and individual inclusion.

Chapter 4 - Internal composition of mineral fluid inclusions

Mineral fluid inclusions have very complicated internal compositions, which are closely related to the type of deposit, the ore-forming environment, and the geological evolution at the late stage of inclusion formation. This chapter introduces the internal composition of mineral fluid inclusions. It takes some ore deposits in China for examples to illustrate the gaseous-phase composition, liquid-phase composition, and solid-phase composition of the inclusions in these deposits. By the end of the chapter, it focuses on the metal components in fluid inclusions, including the analysis and calculation method of heavy metal elements in ore-forming fluids, metal components in fluid inclusions of Cu–Au mineral, metal components in the fluid inclusions of Pb–Zn mineral, and metal components of group inclusions in quartz and pyrite.

Chapter 5 - Component release of fluid inclusions in sulfide mineral

This chapter introduces the component release of fluid inclusions in sulfide minerals, including chalcopyrite, sphalerite, galena, and pyrite and some associated minerals such as quartz. It starts by giving an overview of the mineral raw materials and the methods used for research on fluid inclusions. It then introduces the morphology and component release of fluid inclusions in various sulfide minerals and some associated minerals. The morphology study includes the imaging, size, phase state, and abundance of fluid inclusions using infrared optical microscopic analysis, scanning electron microscopy/energy-dispersive X-ray spectroscopy, and high-resolution X-ray microfault three-dimensional imaging analysis. The component release of fluid inclusions involves the grinding of minerals, component liquid extraction by ultrasonic washing, and liquid-phase analysis using inductively coupled plasma mass spectrometry and ion chromatography.

Chapter 6 - Solubility of sulfide mineral and chemical behaviors of solution after release of inclusion components

This chapter introduces the solubility of sulfide mineral and the chemical behavior of the solution after the release of inclusion components. It starts by explaining the solubility characteristics of sulfide minerals, including experimental dissolution and theoretical calculation of the solubility of the sulfide minerals. It then analyzes the important contribution of the components in fluid inclusions of sulfide mineral to the metal ion system in the pulp by comparing the metal ion concentrations released from the oxidative dissolution of sulfide minerals and that of inclusions. At the end of the chapter, we illustrate the chemical behavior of the Cu2+, Pb2+, and Zn2+ released from mineral inclusions and oxidative dissolution of sulfide minerals by a chemical equilibrium calculation.

Chapter 7 - Interactions among components of fluid inclusions in sulfide mineral, mineral surfaces, and collectors

This chapter introduces the interactions among the components of fluid inclusions, mineral surfaces, and collectors from macroscopic study to the microcosmic aspect. It starts by introducing the adsorption of released components of inclusions on mineral surfaces measured by the ζ potential. It then uses density functional theory to simulate the mechanisms of interactions between components of inclusions and mineral surfaces, including the crystal model and calculation method, surface relaxation and reconstitution of sulfide mineral, and interaction of sulfide surface and Cu components released from fluid inclusions. Further, it introduces the interaction of the collector (xanthate) with Cu-adsorbed sulfide surfaces such as chalcopyrite and sphalerite. At the end of the chapter, it summarizes the effects of fluid inclusion release on the flotation of sulfide minerals, including the effect on the flotation separation, the effect on the chemical system of the sulfide mineral flotation solution, and the effect on the difference in mineral floatability.

Wichmann, C., Chhallani, M., Bocklitz, T., Rösch, P., Popp, J., 2019. Simulation of transportation and storage and their influence on Raman spectra of bacteria. Analytical Chemistry 91, 13688-13694.


Recently, Raman spectroscopy has become more and more in the focus of bacterial identification as it is a culture-independent, nondestructive, and contact-less method. Since Raman spectroscopy is a phenotypic method, lots of parameters can influence the spectra. One of the least controllable factors is transport and storage, but it is often not taken into account, and therefore these influences on the Raman spectra of bacteria are unknown. In order to investigate this effect, we simulated the transport and storage of bacteria under different conditions and investigated them with Raman spectroscopy. With a look at the mean spectra, only one bacterium showed differences during the storage conditions. However, after applying chemometric methods, changes in the data could be found within all bacteria during storage times. This study shows how drastic the effect will influence a database, depending on the different handling or storage. Therefore, it is of the utmost importance to consider these nonbiological influences when planning further experiments and evaluating the resulting data.

Wichmann, J., Lauersen, K.J., Kruse, O., 2020. Green algal hydrocarbon metabolism is an exceptional source of sustainable chemicals. Current Opinion in Biotechnology 61, 28-37.


Microalgae are rapidly growing, low-input requiring, sun light-utilizing microorganisms capable of converting carbon dioxide into various natural products, a major portion of which are hydrocarbons. Their cellular compartmentalization and photosynthetic apparatus depend on robust turnover of two hydrocarbon classes, isoprenoids and acyl-lipids. This review summarizes the current understanding of algal hydrocarbon metabolism, including carbon partitioning capacities, the localization and size of precursor pools, environmental effects on flux distribution, and limiting factors towards efficient (heterologous) hydrocarbon production. Questions and challenges regarding our knowledge of algal hydrocarbon metabolism as well as guidelines for systematic engineering are presented. Recent engineering achievements indicate fundamental plasticity in the (heterologous) hydrocarbon metabolism of green algae while highlighting their potential as renewable sources of these products.

Wilks, J.M., Chen, F., Clark, B.C., Schneegurt, M.A., 2019. Bacterial growth in saturated and eutectic solutions of magnesium sulphate and potassium chlorate with relevance to Mars and the ocean worlds. International Journal of Astrobiology 18, 502-509.

https://doi.org/10.1017/S1473550418000502

Liquid water on Mars might be created by deliquescence of hygroscopic salts or by permafrost melts, both potentially forming saturated brines. Freezing point depression allows these heavy brines to remain liquid in the near-surface environment for extended periods, perhaps as eutectic solutions, at the lowest temperatures and highest salt concentrations where ices and precipitates do not form. Perchlorate and chlorate salts and iron sulphate form brines with low eutectic temperatures and may persist under Mars near-surface conditions, but are chemically harsh at high concentrations and were expected to be incompatible with life, while brines of common sulphate salts on Mars may be more suitable for microbial growth. Microbial growth in saturated brines also may be relevant beyond Mars, to the oceans of Ceres, Enceladus, Europa and Pluto. We have previously shown strong growth of salinotolerant bacteria in media containing 2M MgSO4 heptahydrate (~50% w/v) at 25°C. Here we extend those observations to bacterial isolates from Basque Lake, BC and Hot Lake, WA, that grow well in saturated MgSO4 medium (67%) at 25°C and in 50% MgSO4 medium at 4°C (56% would be saturated). Psychrotolerant, salinotolerant microbes isolated from Basque Lake soils included Halomonas and Marinococcus, which were identified by 16S rRNA gene sequencing and characterized phenetically. Eutectic liquid medium constituted by 43% MgSO4 at −4°C supported copious growth of these psychrotolerant Halomonas isolates, among others. Bacterial isolates also grew well at the eutectic for K chlorate (3% at −3°C). Survival and growth in eutectic solutions increases the possibility that microbes contaminating spacecraft pose a contamination risk to Mars. The cold brines of sulphate and (per)chlorate salts that may form at times on Mars through deliquescence or permafrost melt have now been demonstrated to be suitable microbial habitats, should appropriate nutrients be available and dormant cells become vegetative.

Wilson, J., Ucharm, G., Beman, J.M., 2019. Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem. Scientific Reports 9, 16114.

https://doi.org/10.1038/s41598-019-52430-z

Dissolved oxygen (DO) concentrations shape the biogeochemistry and ecological structure of aquatic ecosystems; as a result, understanding how and why DO varies in space and time is of fundamental importance. Using high-resolution, in situ DO time-series collected over the course of a year in a novel marine ecosystem (Jellyfish Lake, Palau), we show that DO declined throughout the marine lake and subsequently recovered in the upper water column. These shifts were accompanied by variations in water temperature and were correlated to changes in wind, precipitation, and especially sea surface height that occurred during the 2015–2016 El Niño-Southern Oscillation event. Multiple approaches used to calculate rates of community respiration, net community production, and gross primary production from DO changes showed that DO consumption and production did not accelerate nor collapse; instead, their variance increased during lake deoxygenation and recovery, and then stabilized. Spatial and temporal variations in rates were significantly related to climatic variability and changes in DO, and causality testing indicated that these relationships were both correlative and causative. Our data indicate that climatic, physical, and biogeochemical properties and processes collectively regulated DO, producing linked feedbacks that drove DO decline and recovery.

Winding, A., Modrzyński, J.J., Christensen, J.H., Brandt, K.K., Mayer, P., 2019. Soil bacteria and protists show different sensitivity to polycyclic aromatic hydrocarbons at controlled chemical activity. FEMS Microbiology Letters 366.


This study linked growth inhibition of soil bacteria and protists to the chemical activity (a) of polycyclic aromatic hydrocarbons (PAHs) and compared the sensitivities of bacteria and protists. Passive dosing from pre-

loaded silicone provided well-defined and constant a of PAHs in independent tests. Single-species growth inhibition with two bacterial (Pseuodomonas fluorescens DR54 and Sinorhizobium meliloti) and two protist (Cercomonas longicauda and Acanthamoeba castellanii) strains at maximum a (amax) of nine and four PAHs, respectively, showed no inhibition of PAHs with amax below 0.1 (pyrene and anthracene), while growth inhibition was observed for PAHs with amax above 0.1 (e.g. fluorene, fluoranthene and naphthalene). The bacteria were less sensitive than the protists. Soil bacterial community-level growth inhibition by naphthalene was in good agreement with single-species data, but also indicated the presence of sensitive bacteria that were inhibited by a below 0.05 and increasing pre-exposure time giving higher inhibition. The a of 50% inhibition (Ea50) was 0.434 and 0.329 for 0.5 and 4 h pre-exposure time, respectively. Invertebrates tended to be more sensitive than single-celled organisms tested here. This suggests that PAH exposure leads to differential toxicity in soil biota, which may affect soil food web structure and cycling of organic matter.

Wirth, M.A., Sievers, M., Habedank, F., Kragl, U., Schulz-Bull, D.E., Kanwischer, M., 2019. Electrodialysis as a sample processing tool for bulk organic matter and target pollutant analysis of seawater. Marine Chemistry 217, 103719.


Electrodialysis (ED) is an advancing seawater sample processing tool that enables the separation of analytes from the often interfering salt matrix. In this study, we present the evaluation of a laboratory scale ED system for both dissolved organic matter (DOM) and target pollutant analysis of seawater.

The developed sample processing protocol yields reproducible data and was found to be robust towards moderate changes in sample composition. At the final salinity of 0.1, the average recovery of DOM in the form of dissolved organic carbon, nitrogen and phosphorus (DOC, DON and DOP) was 44, 53 and 89%, respectively. DOM loss occurred mainly in the late stage of the ED process.

When investigating specific ED processing parameters, it was discovered that the initial sample salinity does not influence DOM recovery. The final salinity, by contrast, is a dominant influence factor on DOM recovery. Furthermore, DOC and DOP recoveries could be improved by 8% by refining the electrical current in the ED cell. Surprisingly, adjustments of the sample pH did not lead to any improvements in DOM recovery.

The experiments with target analytes showed that the recovery of individual molecules is determined by their n-octanol water partition coefficients logKow. High recoveries > 80% were achieved for compounds with medium logKow of −1 to 3. Hydrophobic compounds with logKow > 3 were lost through surface adsorption to the system walls and tubing. Small, polar and charged compounds with logKow < −1 are prone to loss via ED membrane passage, which occurred predominantly in the late stage of the ED process. Consequently, sample processing with ED was deemed beneficial for the LC-MS or GC–MS analysis of polar target compounds, because they are often difficult to enrich from seawater. Furthermore, during LC-MS or GC–MS analyses, matrix-dependent ion suppression was reduced in ED isolates, giving rise to increased signal responses of 25 to 620%, which resulted in improved instrumental sensitivity.

Witkowski, C.R., Agostini, S., Harvey, B.P., van der Meer, M.T.J., Sinninghe Damsté, J.S., Schouten, S., 2019. Validation of carbon isotope fractionation in algal lipids as a pCO2 proxy using a natural CO2 seep (Shikine Island, Japan). Biogeosciences 16, 4451-4461.


Carbon dioxide concentrations in the atmosphere play an integral role in many Earth system dynamics, including its influence on global temperature. The past can provide insights into these dynamics, but unfortunately reconstructing long-term trends of atmospheric carbon dioxide (expressed in partial pressure; pCO2) remains a challenge in paleoclimatology. One promising approach for reconstructing past pCO2 utilizes the isotopic fractionation associated with CO2 fixation during photosynthesis into organic matter (εp). Previous studies have focused primarily on testing estimates of εp derived from the δ13C of species-specific alkenone compounds in laboratory cultures and mesocosm experiments. Here, we analyze εp derived from the δ13C of

more general algal biomarkers, i.e., compounds derived from a multitude of species from sites near a CO2 seep off the coast of Shikine Island (Japan), a natural environment with CO2 concentrations ranging from ambient (ca. 310 µatm) to elevated (ca. 770 µatm) pCO2. We observed strong, consistent δ13C shifts in several algal biomarkers from a variety of sample matrices over the steep CO2 gradient. Of the three general algal biomarkers explored here, namely loliolide, phytol, and cholesterol, εp positively correlates with pCO2, in agreement with εp

theory and previous culture studies. pCO2 reconstructed from the εp of general algal biomarkers show the same trends throughout, as well as the correct control values, but with lower absolute reconstructed values than the measured values at the elevated pCO2 sites. Our results show that naturally occurring CO2 seeps may provide useful testing grounds for pCO2 proxies and that general algal biomarkers show promise for reconstructing past pCO2.


https://doi.org/10.1007/s00216-019-02065-w

We present an automatically and autonomously operating online laboratory equipped with laboratory chromatographs as an example of Analytics 4.0. At BASF’s largest production site in Ludwigshafen, Germany, multiple GC, HPLC, and IC systems are used in a mostly unstaffed laboratory for automated wastewater monitoring. The purpose of the online system is to prevent unwanted discharges of organic compounds into the wastewater treatment plant and thus protection of the river Rhine. By use of different chromatography and sample preparation techniques, a wide spectrum of compounds can be quantitatively assessed. Most analyzers are coupled to mass spectrometers, and all are equipped with robotic autosamplers. Mixed wastewater samples are collected automatically at 20-min intervals and distributed to the instruments. To operate the online system 24/7, sensors, visualization tools, special software packages, remote access tools, and other assistance systems are required. Many of the software features are as yet not commercially available and thus had to be developed and programmed in-house since they are required in an Analytics 4.0 environment.



To examine the bioavailability of dissolved organic carbon (DOC) and nitrogen (DON) in riverine dissolved organic matter (DOM) discharged to the coastal ocean, we conducted a series of month-long (24 days) incubation experiments with filtered samples collected from five southern Texas rivers (Lavaca, San Antonio, Mission, Aransas, and Nueces) inoculated using the same natural coastal microbial assemblages during summer (June) and winter (January) in 2016. The bioavailable fractions of DOC and DON (BDOC% and BDON%) varied substantially in different rivers and seasons, ranging respectively from 6–11% and 15–38% during winter, and 0–6% and 9–15% during summer. Relatively higher BDOC% and BDON% occurred in the San Antonio and Aransas Rivers, which are impacted more by human activities through discharge from wastewater treatment plants. Seasonally, the riverine DOM was more bioavailable in winter than in summer when DOM may have been extensively degraded in situ due to the low base flow (or long residence time) and the elevated temperature in river water in summer. The principal component analysis on amino acid composition further confirmed that DOM was less degraded in winter than in summer. Functional gene abundance data revealed that winter riverine DOM was relatively labile as evidenced by an increase in N-metabolism pathways and functional genes during the winter incubation, whereas the opposite pattern was observed in summer. The findings of the varying bioavailability of DOM among rivers and seasons have important implications about the fate of riverine DOM and their potential contributions to nutrient supplies as southern Texas bays and estuaries are often nitrogen limited.

Wu, K., Tian, L., Liang, L., Metcalfe, I., Chu, D., Tong, J., 2019. Recurrent biotic rebounds during the Early Triassic: biostratigraphy and temporal size variation of conodonts from the Nanpanjiang Basin, South China. Journal of the Geological Society 176, 1232.


Eleven conodont zones are established for the Lower Triassic of the Motianling section in the Nanpanjiang Basin, South China. Detailed size measurements on 2244 P1 conodont elements demonstrate dynamic size variation patterns during the Early Triassic that are calibrated to the Early Triassic timescale and conodont zonation. Correlation of conodont size variation with various environmental indicators shows that these size changes are primarily controlled by rapidly changing and episodic environmental conditions and ecological recovery in the aftermath of the end-Permian mass extinction. Decreasing size trends occur in the early Griesbachian, late Griesbachian and at the Smithian–Spathian boundary. Episodes of size increase (rebounds) occur in the middle Griesbachian, Induan–Olenekian boundary and middle–late Spathian. The observed temporal size variations indicate that conodont animals were significantly affected by rapidly changing environmental conditions (mainly temperature and redox conditions) during the Early Triassic and recurrent size increases (rebounds) occurred during periods of environmental and climatic amelioration (climatic cooling and oxygenation), demonstrating a complicated recovery history of marine ecosystems in the aftermath of the largest Phanerozoic biotic crisis.Supplementary material: Data for all species are available at https://doi.org/10.6084/m9.figshare.c.4528616

Wu, S., Zhou, Y., Gerngross, D., Jeschek, M., Ward, T.R., 2019. Chemo-enzymatic cascades to produce cycloalkenes from bio-based resources. Nature Communications 10, 5060.

https://doi.org/10.1038/s41467-019-13071-y

Engineered enzyme cascades offer powerful tools to convert renewable resources into value-added products. Man-made catalysts give access to new-to-nature reactivities that may complement the enzyme’s repertoire. Their mutual incompatibility, however, challenges their integration into concurrent chemo-enzymatic cascades. Herein we show that compartmentalization of complex enzyme cascades within E. coli whole cells enables the simultaneous use of a metathesis catalyst, thus allowing the sustainable one-pot production of cycloalkenes from oleic acid. Cycloheptene is produced from oleic acid via a concurrent enzymatic oxidative decarboxylation and ring-closing metathesis. Cyclohexene and cyclopentene are produced from oleic acid via either a six- or eight-step enzyme cascade involving hydration, oxidation, hydrolysis and decarboxylation, followed by ring-closing metathesis. Integration of an upstream hydrolase enables the usage of olive oil as the substrate for the production of cycloalkenes. This work highlights the potential of integrating organometallic catalysis with whole-cell enzyme cascades of high complexity to enable sustainable chemistry.

Wu, Y., Jiang, Z., Lu, X., Liang, Y., Wang, H., 2019. Domino electroreduction of CO2 to methanol on a molecular catalyst. Nature 575, 639-642.

https://doi.org/10.1038/s41586-019-1760-8

Electrochemical carbon dioxide (CO2) reduction can in principle convert carbon emissions to fuels and value-added chemicals, such as hydrocarbons and alcohols, using renewable energy, but the efficiency of the process is limited by its sluggish kinetics. Molecular catalysts have well defined active sites and accurately tailorable structures that allow mechanism-based performance optimization, and transition-metal complexes have been extensively explored in this regard. However, these catalysts generally lack the ability to promote CO2 reduction beyond the two-electron process to generate more valuable products. Here we show that when immobilized on carbon nanotubes, cobalt phthalocyanine—used previously to reduce CO2 to primarily CO—catalyses the six-electron reduction of CO2 to methanol with appreciable activity and selectivity. We find that the conversion, which proceeds via a distinct domino process with CO as an intermediate, generates methanol with a Faradaic efficiency higher than 40 per cent and a partial current density greater than 10 milliamperes per square centimetre at −0.94 volts with respect to the reversible hydrogen electrode in a near-neutral electrolyte. The catalytic activity decreases over time owing to the detrimental reduction of the phthalocyanine ligand, which can be suppressed by appending electron-donating amino substituents to the phthalocyanine ring. The improved molecule-based electrocatalyst converts CO2 to methanol with considerable activity and selectivity and with stable performance over at least 12 hours.

News & Views https://www.nature.com/articles/d41586-019-03563-8

Wu, Y., Zhu, K., Zhang, J., Müller, M., Jiang, S., Mujahid, A., Muhamad, M.F., Sia, E.S.A., 2019. Distribution and degradation of terrestrial organic matter in the sediments of peat-draining rivers, Sarawak, Malaysian Borneo. Biogeosciences 16, 4517-4533.


Tropical peatlands are one of the largest pools of terrestrial organic carbon (OCterr); however, our understanding of the dynamics of OCterr in peat-draining rivers remains limited, especially in Southeast Asia. This study used bulk parameters and lignin phenol concentrations to investigate the characteristics of OCterr in a tropical peat-draining river system (the main channel of the Rajang and three smaller rivers: the Maludam, Simunjan, and Sebuyau) in the western part of Sarawak, Malaysian Borneo. The depleted δ13C levels and lignin composition of the organic matter indicates that the most important plant source of the organic matter in these rivers is woody angiosperm C3 plants, especially in the three small rivers sampled. The diagenetic indicator ratio, i.e., the ratio of acid to aldehyde of vanillyl phenols ((Ad∕Al)V), increased with decreasing mean grain size of sediment from the small rivers. The selective sorption of acid relative to aldehyde phenols might explain the variations in the (Ad∕Al)V ratio. Elevated (Ad∕Al)V values observed from the Maludam's sediments may also be attributed to source plant variations. The (Ad∕Al)V ratio appears to be related to the C∕N ratio (the ratio of total organic carbon to total nitrogen) in the Rajang and small rivers. In small rivers, a quick decline of C∕N ratios is a response to the slower modification of (Ad∕Al)V ratios due to better preservation of lignin phenols. An accumulation of lignin phenols with higher total nitrogen percentages (TN%) in the studied systems was observed. Most of the OCterr discharged from the Rajang and small river systems was material derived from woody angiosperm plants with limited diagenetic alteration before deposition and thus could potentially provide significant carbon to the atmosphere after degradation.

Xiao, P., Lv, C., Wang, R., Cui, M., Xu, Q., Hu, Q., Hu, W., 2019. Laboratory study heterogeneity impact on microscopic residual oil distribution in tight sandstone cores during CO2 immiscible flooding. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 2895-2905.

https://doi.org/10.1080/15567036.2019.1582732

We use physical simulation experiment and nuclear magnetic resonance methods to investigate crude oil distribution after immiscible CO2 flooding schemes in tight sandstone cores. Experimental results indicate that water-wet cores lead to the highest final recovery factor in comparison with intermediate wet cores and weak oil-wet cores, and the recovery oil difference in clay micropore is mainly because of the heterogeneity, and the difference in medium pore and large pore is affected by asphaltene precipitation phenomenon. Therefore, it is important to enhance the recovery in the clay micropores and reduce the impact of cores permeability reduction caused by asphaltene precipitation. Based on this investigation on the residual oil saturation in pore throats, immiscible CO2 flooding can be a potential method to improve recovery efficiency in tight oil reservoir.

Xiong, W., Bian, X.-Q., Liu, Y.-B., 2020. Phase equilibrium modeling for methane solubility in aqueous sodium chloride solutions using an association equation of state. Fluid Phase Equilibria 506, 112416.


A new formulation for the fraction of electron acceptor sites of methane (CH4) of cubic-plus-association couple with Huron-Vidal (CPA-HV) model is presented, and a combine rule is used to calculate the cross-associating strength of CH4-water (H2O) binary system. Meanwhile, the interaction parameters (Eij, Eji and F) of CPA-HV model are regressed for CH4–H2O binary and CH4–H2O–NaCl ternary systems. The predictions of CPA-HV model are consistent with a lot of binary and ternary experimental data of these systems. Compared with CPA-vdW and SRK-HV models, the accuracy of CPA-HV model is the best for vapor-liquid equilibria of CH4–H2O system. The average absolute relative deviations of the predicted CH4 solubility in H2O and aqueous sodium chloride solutions for CPA-HV model are respectively 5.84% and 6.91%.

Xu, H., 2020. Probing nanopore structure and confined fluid behavior in shale matrix: A review on small-angle neutron scattering studies. International Journal of Coal Geology 217, 103325.


Although continued growth in unconventional oil and gas production is generally projected, its long-term growth potential and sustainability have significant uncertainties. A critical problem is the low hydrocarbon recovery rates from shale and other tight formations using the horizontal well drilling and hydraulic fracturing techniques: < 10% for tight oil and ~ 20% for shale gas. Moreover, the production rate for a given well typically declines rapidly within one year. The low recoveries and declining production of shale oil and gas reservoirs are apparently related to the small porosity (a few to a few hundred nm) and low permeability (10−16–10−20 m2) of shale matrix, which make the enclosed hydrocarbon fluids difficult to access. Hence, to enhance the hydrocarbon recovery from shale matrix, it is essential to study its nanopore structure and confined fluid behavior.

Small- and ultra-small-angle neutron scattering (SANS and USANS) have emerged as a powerful method for characterizing shale nanopore structure and confined fluid behavior. Owing to neutrons' high penetrating ability and high sensitivity to hydrogen (and its isotope, deuterium), SANS/USANS can probe inside shale samples to characterize nanopores from 1 nm to 10 μm in size and be readily combined with sample environmental cells to examine the fluid (hydrocarbon and water – frack fluid) behavior at relevant pressure-temperature (P-T) conditions. In this review article, an introduction is first given on the characteristics of shale matrix and the uniqueness of SANS/USANS compared with conventional methods. Then current studies on shale nanopore structure and confined fluid properties using SANS/USANS are summarized. Finally, an outlook and perspective on future research in this emerging area will be offered.

Xu, S., Ma, J., Ji, R., Pan, K., Miao, A.-J., 2020. Microplastics in aquatic environments: Occurrence, accumulation, and biological effects. Science of The Total Environment 703, 134699.


Microplastics, whether originating directly from industrial and household products or from the degradation of larger plastics, are currently of intense global concern. These particles are present in aquatic environments in high concentrations and may adversely affect aquatic organisms. An additional concern is the ability of microplastics to adsorb inorganic and organic pollutants and subsequently liberate them into marine and freshwater systems. In this review, we report on the occurrence and abundance of microplastics in the global aquatic environment. We then consider the accumulation (uptake, distribution, and elimination) of microplastics in aquatic organisms and the important factors that lead to bioaccumulation. The effects of microplastics on aquatic organisms of different trophic levels are also discussed. Several studies have shown that the size, shape, and surface physicochemical characteristics of microplastics are essential determinants of their biological effects. Finally, we examine the combined effects of microplastics and other pollutants, including persistent organic pollutants and heavy metals. Our review concludes by suggesting future lines of research based on the remaining knowledge gaps in microplastic research.

Yadav, U.S., Shukla, K.M., Ojha, M., Kumar, P., Shankar, U., 2019. Assessment of gas hydrate accumulations using velocities derived from vertical seismic profiles and acoustic log data in Krishna-Godavari Basin, India. Marine and Petroleum Geology 108, 551-561.


The second Indian National Gas Hydrate Program Expedition (NGHP-02) was executed in 2015 in four areas termed as Areas A, B, C and E. During this expedition, twenty five research sites were drilled and/or cored in Krishna-Godavari (KG) and Mahanadi Basins, eastern Indian offshore. During NGHP-02, zero offset vertical seismic profile (VSP) data were acquired at three sites: Sites NGHP-02-17, −19 and −22 in Area B of the KG

Basin. In this study, we focus on the three sites in Area B of the KG Basin, where, zero-offset VSP and downhole acoustic log data are used to assess and characterize the gas hydrate deposits. Zero-offset VSP data are correlated with wireline log, surface seismic and synthetic seismic data to characterize and delineate gas hydrate accumulations in the KG Basin. Low velocities ranging from 1500 to 1650 m/s are observed in the unconsolidated shallow sedimentary section above gas hydrate-bearing units, whereas, very high velocities are observed in the acquired acoustic log and VSP data. In the gas hydrate-bearing sedimentary sections, the VSP derived interval velocities range from 2000 to 3000 m/s in the depth interval between 267 and 287 m below sea floor (mbsf) at Site NGHP-02-17, between 1650 and 1750 m/s in the depth interval between 306 and 366 mbsf at Site NGHP-02-19 and between 1700 and 1800 m/s in the depth interval between 198 and 290 mbsf at Site NGHP-02-22. Gas hydrates are distributed both as pore-filling and fracture-filling at all three sites, however, high concentrations are only observed as pore-filling morphology. We estimate the amount of gas hydrate considering both isotropic (pore-filling) and anisotropic (fracture-filling) acoustic reservoir models. Our estimations of gas hydrate saturation match well with the available pressure core data and suggest that high gas hydrate concentrations (to nearly 85% of pore space) are distributed in a load bearing morphology.

Yaghmour, F., 2019. Are oil spills a key mortality factor for marine turtles from the eastern coast of the United Arab Emirates? Marine Pollution Bulletin 149, 110624.


Though relatively rare events, oil spills can have devastating impacts on marine resources. In this study, from August 2015 to December 2018, we monitor turtle strandings/mortalities as well as nearshore oil spills on the eastern coast of the United Arab Emirates to determine if they are linked. This involved 73 marine turtle strandings of four species and 17 oil spills. The results show an increase in stranding frequency after a spill enters shallow coastal waters. Months with lower oil spill frequencies had fewer strandings, while months with higher spill frequencies were associated with more strandings. 31.9% of all strandings were discovered within 10 days following a spill. Additionally, some of these stranded turtles showed signs of interaction with oil, including oil on and inside their bodies and positive buoyancy disorders. The results suggest that oil spill frequency may have an important influence on marine turtle health in the Gulf of Oman coast of the UAE.

Yan, S.M., McCoy, R.C., 2019. Functional divergence among hominins. Nature Ecology & Evolution 3, 1507-1508.

https://doi.org/10.1038/s41559-019-0995-y

Inferred gene expression differences between modern humans and our extinct archaic relatives suggest potential mechanistic bases for the evolution of hominin phenotypes.

Yan, Y., Bender, M.L., Brook, E.J., Clifford, H.M., Kemeny, P.C., Kurbatov, A.V., Mackay, S., Mayewski, P.A., Ng, J., Severinghaus, J.P., Higgins, J.A., 2019. Two-million-year-old snapshots of atmospheric gases from Antarctic ice. Nature 574, 663-666.

https://doi.org/10.1038/s41586-019-1692-3

Over the past eight hundred thousand years, glacial–interglacial cycles oscillated with a period of one hundred thousand years (‘100k world’). Ice core and ocean sediment data have shown that atmospheric carbon dioxide, Antarctic temperature, deep ocean temperature, and global ice volume correlated strongly with each other in the 100k world. Between about 2.8 and 1.2 million years ago, glacial cycles were smaller in magnitude and shorter in duration (‘40k world’7). Proxy data from deep-sea sediments suggest that the variability of atmospheric carbon dioxide in the 40k world was also lower than in the 100k worl, but we do not have direct observations of atmospheric greenhouse gases from this period. Here we report the recovery of stratigraphically discontinuous ice more than two million years old from the Allan Hills Blue Ice Area, East Antarctica. Concentrations of carbon dioxide and methane in ice core samples older than two million years have been altered by respiration, but some younger samples are pristine. The recovered ice cores extend direct observations of atmospheric carbon dioxide, methane, and Antarctic temperature (based on the deuterium/hydrogen isotope ratio δDice, a

proxy for regional temperature) into the 40k world. All climate properties before eight hundred thousand years ago fall within the envelope of observations from continuous deep Antarctic ice cores that characterize the 100k world. However, the lowest measured carbon dioxide and methane concentrations and Antarctic temperature in the 40k world are well above glacial values from the past eight hundred thousand years. Our results confirm that the amplitudes of glacial–interglacial variations in atmospheric greenhouse gases and Antarctic climate were reduced in the 40k world, and that the transition from the 40k to the 100k world was accompanied by a decline in minimum carbon dioxide concentrations during glacial maxima.

Yang, C., Wang, S., Ren, M., Li, Y., Song, W., 2019. Hydrothermal liquefaction of an animal carcass for biocrude oil. Energy & Fuels 33, 11302-11309.


This study investigated the optimum operating conditions on hydrothermal liquefaction (HTL) for the production of biocrude oil from an animal carcass. HTL experiments were carried out at various reaction temperatures (230–350 °C), residence times (10–80 min), solid concentrations (5–20 wt %), and pressures (15–30 MPa). Detailed chemical composition analysis of biocrude oil was performed by gas chromatography–mass spectrometry, Fourier transform infrared spectroscopic analysis, and element analysis. The results showed that the biocrude oil was composed of fatty acids, hydrocarbons, amides, esters, and N-heterocyclic compounds. The maximum biocrude oil yield of 55.6 wt % was obtained at 320 °C and 10 wt % solid concentration for a residence time of 60 min. Pressure imparts little on the yield of biocrude oil. The higher heating value of the biocrude oil ranging from 39.7 to 42.5 MJ kg–1 was comparable to that of petroleum crude (42.9 MJ kg–1). In addition, the general reaction pathways for HTL of an animal carcass were proposed. The results of this study demonstrated that HTL is a promising method for disposal of an animal carcass for the production of biocrude oil.

Yang, H., Li, Y., Tang, Y., Lei, G., Sun, X., Zhou, P., Zhou, L., Xu, A., Tang, J., Zhu, W., Shang, J., Chen, W., Li, M., 2019. Reservoir accumulation conditions and key exploration & development technologies for Keshen gas field in Tarim Basin. Petroleum Research 4, 295-313.


The Keshen gas field is located in the central part of Kuqa foreland thrust belt in Tarim Basin, and is another large gas field discovered in Kuqa depression after Kela 2 gas field. Since the breakthrough in 2008, a number of large and medium scale gas reservoirs including Keshen 2, Keshen 5 and Keshen 8 have been discovered, that are characterized by ultra depth, ultra-high pressure, ultra-low porosity, ultra-low permeability, high temperature and high pressure. With natural gas geological reserves of nearly trillion cubic meters and production capacity of nearly 5.5 billion cubic meters, the Keshen gas field is the main natural gas producing area in Tarim Oilfield. The Keshen gas field is located in a series of thrusting imbrication structures in the Kelasu structural belt of Kuqa foreland thrust belt. The salt roof structure, plastic rheology of salt beds and pre-salt faulted anticlinal structure constitute the large wedge-shaped thrust body. The thick delta sandstone of the Cretaceous Bashijike Formation is widely distributed, and it forms the superior reservoir-caprock combination with overlying Paleogene thick gypsum-salt bed. The deep Jurassic-Triassic oil and gas migrate vertically along fault system formed in Late Himalaya, break through the thick Cretaceous mudstone and move laterally along the fracture system of the pre-salt reservoirs, to form anticline and fault anticline high pressure reservoir groups. Through near ten years of studies, the three-dimensional seismic acquisition and processing technology for complex mountainous areas, extrusion salt-related structural modeling technology and fractured low-porosity sandstone reservoir evaluation technology have been established, which lay a foundation for realization of oil and gas exploration objectives. Logging acquisition and evaluation technology for high temperature, high pressure, ultra-deep and low-porosity sandstone gas reservoirs, and efficient development technology for fractured tight sandstone gas reservoirs have been developed, which provide a technical support for efficient exploration & development and rapid production of the Keshen gas field.

Yang, Y., Lun, Z., Wang, R., Hu, W., 2020. Non-equilibrium phase behavior in gas condensate depletion experiments. Fluid Phase Equilibria 506, 112410.


Full diameter core depletion tests are performed in this study to investigate the influence of depletion rate on the production of gas and condensate. Experimental results confirm that the gas recovery of the fast-depletion test is lower than that of the slow-depletion test. On the contrary, without the consideration of the fluid flow in porous media, the condensate recovery of the fast-depletion test is higher than that of the slow-depletion test.

Non-equilibrium phase behavior is claimed to explain this abnormal behavior. The non-equilibrium model is adopted in this paper based on the components’ transfer rates between oil and gas phases. In addition, with the consideration of the compositional change in gas-condensate production, a numerical model is built to simulate the depletion process. Based on the comparison between the simulation and experimental results, the influence of non-equilibrium phase behavior on gas-condensate production is analyzed. If the depletion rate is relatively high, the heavy components of the gas-condensate system tend to be produced within the gas phase instead of condensing inside the core due to incomplete vapor-liquid separation. As a result, more condensate is acquired from the fast-depletion test.

Yang, Y., Su, X., Fan, Z., Wang, D., Li, J., 2020. Numerical investigation of naphthalene deposition dynamics during CO2 leakage. International Journal of Greenhouse Gas Control 92, 102860.


An important leakage risk associated with CO2 geological sequestration is the potential transport and fate of organic contaminants due to the CO2 leakage. In this paper, a precipitation and deposition dynamic model was constructed using COMSOL to evaluate the potential impacts of organic contaminants in response to the leakage of CO2 and brine into a shallow aquifer. The Span-Wagner equation and Peng-Robinson equations were adopted to estimate the partitioning behavior of organic contaminants. Numerical simulations with naphthalene as a representative contaminant show that the dissolved component is transported with the equilibrium concentrations at the thermodynamic conditions built by the fluid phase, while the precipitated solid particles are either transported with carrier fluid or deposited in the leakage pathway according to the deposition dynamic model. The sharp decrease of solubility promotes the precipitation impetus while the deposition rate mainly depends upon the leakage velocity and pore structure. Local blockage may occur due to the accumulation of deposited particles, and the potential location is most likely to be near the outlet of the leakage pathway in current scenario. Sensitivity analyses indicate that pressure difference and temperature buildup would influence both the leakage velocity and deposition dynamics, while the pore structure of leakage pathway, represented by porosity and permeability, will affect the leakage characteristic so as to the deposition rate. The presented models are generic in nature for naphthalene transport, demonstrating a methodology that can explore the generation of a potential third organic phase in contaminant transport for risk assessments.

Yao, W., Paytan, A., Wortmann, U.G., 2020. Effects of a transient marine sulfur reservoir on seawater δ18OSO4

during the Paleocene-Eocene Thermal Maximum. Geochimica et Cosmochimica Acta 269, 257-269.


Recent work suggests that during the Paleocene-Eocene Thermal Maximum (PETM) the volume of the oceanic oxygen minimum zone (OMZ) has expanded by one order of magnitude and acted as a transient reservoir for reduced sulfur. Fluctuations in the seawater S-isotope ratios (δ34SSO4) can be used to estimate the size of this reservoir, but do not capture the gross fluxes associated with hydrogen sulfide reoxidation at the upper and lower boundaries of the OMZ. Isotope exchange processes during microbially mediated sulfate reduction as well as constant reoxidation of hydrogen sulfide to sulfate, however, affect the oxygen isotope ratio of seawater sulfate (δ18OSO4). Here we present a high-resolution (10-kyr) barite δ18OSO4 record. Our data shows that the δ18OSO4 value increased by 1.5‰ within 48 kyrs from the onset of the PETM and then returned to the pre-excursion value over the next 200 kyrs. Quantitative modeling suggests that the gross microbial sulfate

reduction (MSR) flux was on the order of 4 × 1014 mol/yr, which is about one order of magnitude higher than the gross sulfate reduction flux in the modern ocean.

Yazdani Sadati, E., Sahraei, E., 2019. An experimental investigation on enhancing water flooding performance using oil-in-water emulsions in an Iranian oil reservoir. Journal of Petroleum Exploration and Production Technology 9, 2613-2624.

https://doi.org/10.1007/s13202-019-0679-9

Emulsions are extensively prevalent in the oil industry in both advantageous and disadvantageous ways. In the literature, conventional water flooding in high permeability oil reservoirs has confronted with water channeling and poor sweep efficiency. In this paper, the remedial application of O/W emulsions as an EOR method in improving water performance is discussed. To this purpose, a series of flooding experiments were carried out in one of the Iranian oil reservoirs in reservoir condition of 75 C and 2000 psi. Then, visual stability measurements were conducted to inspect the stability characterization of the emulsion. Sodium dodecyl sulfate was applied helping simple dispersion of the gasoil into the water phase, and emulsions with water percentage of 90, 80, 70 and 60 were developed to introduce into the porous media. It was found out from flooding experiments that emulsion injection after conventional water flooding can lead to additional oil recovery (up to 20%). Besides, the emulsion with 80% water cut was determined as the optimum emulsion for injection in this reservoir considering financial aspects. Moreover, results of the stability test revealed that the aqueous phase with one wt% surfactant or higher had formed emulsions which have been stable during a long period of 6 months.

Yi, H., Norell, M., 2019. The bony labyrinth of Platecarpus (Squamata: Mosasauria) and aquatic adaptations in squamate reptiles. Palaeoworld 28, 550-561.


Mosasaurs were among the last marine reptiles that lived before the Cretacesous–Paleogene extinction. Little is known about the sensory evolution of mosasaurs in relation to their aquatic lifestyle. In this study, the braincase of Platecarpus was CT-scanned and virtual models were constructed showing the bony labyrinth — or the inner ear — a sensory apparatus for balance and hearing. The virtual inner ear consists of the semicircular canals, vestibule, and cochlea. Compared with extant squamates, Platecarpus resembles sea snakes in having a small vestibule with a flat dorsal surface, but it differs from non-mosasaurian squamates in having rounded semicircular canals. Phylogenetic linear regression analysis supports a linear relationship, independent from phylogeny, between the length of the three semicircular canals and the length of the skull. The semicircular canals of Platecarpus are shorter than predicted, but the fossil data fell within the 95% prediction interval calculated from the extant data and the skull length of Platecarpus. Although size reduction of the bony labyrinth has been associated with aquatic adaptions in mammals, our results suggest that in squamates, semicircular canal size is related to skull size rather than habitat preference.



In 1895, X-ray was discovered by the German physicist Wilhelm Conrad Roentgen, and one year later, this invisible light were applied by palaeontologists to study fossils embedded within slates (Hohenstein, 2004). Until today, X-ray radiography as a nondestructive imaging method is still very useful and welcome in detecting fossils which have been buried in rock matrix (Hohenstein, 2004, Kuhl et al., 2009). In 1972, X-ray computed tomography (CT) scanner was invented by Godfrey Hounsfield (Richmond, 2004) providing a more powerful imaging technique for palaeontologists to analyze fossils three dimensionally. Now, industrial CT scanning is widely used in studies of fossilized organisms (Sutton et al., 2014). In addition to industrial CT scanning, several latest nondestructive imaging techniques for three-dimensionally reconstructing and visualizing fossils, including synchrotron radiation X-ray tomographic microscopy (SRXTM) (Donoghue et al., 2006, Tafforeau et al., 2006, Gai et al., 2011, Yin et al., 2014, Yin et al., 2015, Yin et al., 2016, Yin et al.,

2017), X-ray microtomography (micro-CT/μCT) (Hagadorn et al., 2006, Lu et al., 2012, Lu et al., 2016a, Lu et al., 2016b, Lu et al., 2017, Zhu et al., 2016) and three-dimensional X-ray microscopy (3D-XRM) with submicron resolution (Wu et al., 2018, Yin et al., 2018), have played important roles in palaeontological community.

The development of the techniques for visualizing and analyzing fossils in three-dimensions has transformed the study of fossils and yielded a new field, Virtual Palaeontology (Sutton et al., 2014). With the help of these nondestructive and three-dimensional imaging techniques, fossils can provide unprecedented insights into the evolutionary history of life, thereby enhancing our understanding of the present-day biosphere and ecology. The techniques for Virtual Palaeontology are being developed at all time. In order to show the advantages and introduce the recent advances in Virtual Palaeontology, we, therefore, believe that it is quite significant to demonstrate some novel applications of these nondestructive X-ray tomographic techniques (including SRXMT, micro-CT, 3D-XRM) in palaeontology (Table 1). So we organized this special issue, “Virtual Palaeontology: when fossils illuminated by X-ray”, to highlight the new achievements in the understanding of the origin and evolution of key biological clades and/or characters revealed by X-ray.

In this special issue, we present 13 original research articles and one comment paper. Among the 13 research articles, three applied SRXTM (Gai et al., 2019, Huang et al., 2019, Landon et al., 2019), five applied micro-CT (Hu et al., 2019a, Hu et al., 2019b, Lu and Zhu, 2019, Wang et al., 2019, Yi and Norell, 2019), four applied 3D-XRM (Li, D.D. et al., 2019, Shi et al., 2019, Sun et al., 2019, Yu et al., 2019) and one methodological paper focuses on developing iodine staining protocol for CT studies (Li, Z.H. et al., 2019). In each paper, the authors applied cutting-edge imaging techniques and computer-based technologies to reveal the three-dimensional structures of the specimens through interactive digital visualizations. The topics of these 13 articles cover a wide range from invertebrates to vertebrates, from algae to plants, from novel trace to fossil trace, from microfossils to megascopic fossils.

In this issue, Huang et al. (2019) scanned five exceptionally preserved conodont clusters (Nicoraella) from the Triassic Luoping Biota, Yunnan Province, Southwest China using high resolution SRXTM. They present so far, the most complete reconstruction of fused conodont clusters. The new data is not only important for reconstruction of apparatus architecture and understanding element functional kinematics, but also helpful to resolve the classification and phylogeny of Gondolelloidea.

In vertebrate palaeontology, Gai et al. (2019) further describe the circulatory system of Shuyu, a jawless fish closely associated with the rise of jaws by using SRXTM. Their results indicate that the circulatory system of galeaspids exhibits a mosaic of primitive vertebrate and possible gnathostome characters, including a number of derived gnathostome characters that are absent from osteostracans.

Over the past two decades, SRXTM with submicron spatial resolution have transformed the study of the Weng’an biota, a unique taphonomic window of eukaryotes from the early Ediacaran Doushantuo Formation, South China. Landon et al. (2019) scanned a number of millimeter-scale spherical fossils from the Weng’an biota using high resolution SRXTM. Their discovery highlights that the biodiversity of spherical fossils from the Weng’an biota is higher than previously thought. Furthermore, the distinct development mode of Sporosphara guizhouensis, a new eukaryotic species they found, implies an adaption to harsh marine environmental condition where the early eukaryotes lived.

In addition to spherical microfossils, the Ediacaran Weng’an biota also yields four genera tubular microfossils which have ever been widely interpreted as the earliest eumetazoans with possible cnidarian (Xiao et al., 2000, Chen et al., 2002) or multicellular algal affinities (Cunningham et al., 2015). To test the hypotheses, Sun et al. (2019) scanned several branching tubular microfossils from the Weng’an biota using 3D-XRM, and explored the biology and ecology of the four taxa of tubular microfossils in the light of 3D reconstructions, SEM scanning and thin section observations. Sun and colleagues found that there is no evidence to support the animal affinity. Instead, the branching Ramitubus can be compared with algae-like Cambrian Epiphyton, while the non-branching Sinocyclocyclicus, Quadratitubus and Crassitubus are comparable to filamentous cyanobacteria.

In the field of micropalaeontology, it is always a time exhausted work to study the internal structures of microfossils such as fusulinids using traditional methods including SEM scanning and thin section observation. In this issue, for the first time, Shi et al. (2019) present the full three-dimensional visuals of fusulinid

reconstructed by micro-CT and 3D-XRM. Using this case study, the authors argue that using approaches of X-ray tomography, the scientists can acquire the information of morphology and internal structures more precisely and easier. Moreover, 3D visualizing is easier for scientists to understand and exhibit the biology and architecture.

Flatten fossils are not the ideal objects for CT scanning. Li, D.D. et al. (2019) study flatten fossil plant from the Wuda Tuff Flora from Wuda Coalfield of Inner Mongolia, China, by applying 3D-XRM. With the help of high-resolution tomographic reconstruction, the authors present 3D architectures of an ultimate fertile pinna, showing detailed biological information of synangia and sporangia. These information casts new light on the understanding of the new species.

In recent years, the micro-CT has played a quite important role in studying fossil inclusions of the mid-Cretaceous amber from the northern Myanmar. Yu et al. (2019) focus on some gastropods from the Myanmar amber, and described two new species with the help of 3D-XRM reconstruction. Even though the classification of the two species are still controversial (please refer to the comments by Neubauer et al., 2019), this report evidences the high biodiversity documented by the time capsules formed ca. 99 million years ago.

X-ray tomography has been a more and more popular technique of 3D reconstruction and visualization for various kinds of body fossils, however, applying CT for ichnological and neoichnological studies is still in its infancy. In this issue, Wang et al. (2019) scanned modern traces produced by ocypodid crab using industrial micro-CT, and presented abundant I-, U- and Y-shaped burrows with beautiful details. The traces show striking similarities with some fossil traces such as Psilonichnus, indicating a palaeoenvironmental background of coastal and shelf environments for the later.

In vertebrate palaeontology, X-ray tube-aided tomography gained quick popularity once the technology became mature. Hu et al. (2019a) present the detailed anatomy of the gnathal elements in an exquisitely preserved 400 million-year-old buchanosteid arthrodire by high resolution CT. Their work gives insights into the primitive arthrodire condition for comparison with the dermal jaw bones of Chinese ‘maxillate’ placoderms, which are closely associated with the crown-group jawed vertebrates. In another paper of the special issue, Hu et al. (2019b) re-investigate the reconstruction of the shoulder girdle and opercular series of Devonian tetrapodomorph fish Gogonasus andrewsae by uniting micro-CT imaging, reconstruction, visualization and 3-D printing techniques. The authors provide a new way to investigate the constructional morphology of one or more mechanical units of the vertebrate skeleton.

A newly-discovered cranial shield of Pragian (∼410 million years ago, Early Devonian) dipnomorph fish Arquatichthys from Yunnan, South China has been reported based on high resolution CT (Lu and Zhu, 2019). The new morphological details, such as an intricate occipital artery system revealed by high resolution CT for the first time, shed light on the cranial character transformations during the early diversification of lungfish plus tetrapod lineages.

By comparison with a wide range of extant squamates, the bony labyrinth morphology of a mosasaurian squamate Platecarpus has been digitally reconstructed (Yi and Norell, 2019). This work suggests that semicircular canal size in squamates is related to skull size rather than habitat preference.

To enhance the contrast in X-ray tomography, iodine staining method was applied with increasingly popularity. Li, Z.H. et al. (2019) discuss the mechanism of this method, and propose a mass transfer modeling to simulate iodine diffusion, predicting iodine concentrations within distinct tissue types. This work provides key insight into the mechanisms behind the efficacy of solution replenishment in enhancing staining effects.

As a snapshot of the recent X-ray method development and applications in palaeontology, this special issue reveals that Virtual Palaeontology has improved our abilities profoundly to gain a more complete view of fossilized life because of its advantages, such as allowing for 3D visualizing, virtual dissection, segmentation, quantitative studies, threedimensional printing, and specimen sharing.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Jang, J., Waite, W.F., Kumar, P., Tenma, N., 2019. Permeability variation and anisotropy of gas hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 524-536.


Permeability measurements were conducted on gas hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin during India's National Gas Hydrate Program Expedition 02. Pressure cores collected in the deep seabed of the Indian Ocean were cut and stored under high pressure and low temperature on the D/V Chikyu using pressure core analyzing tools. A total of 25, 1.2-m storage chambers were transferred to Japan from India for pressure core studies using pressure-core analysis tools at the National Institute of Advanced Industrial Science and Technology. The sediment core's pressure and temperature were maintained within the hydrate stability conditions during the entire process of transfer and loading into a triaxial testing apparatus called TACTT to preserve the hydrate, which can simulate the in-situ effective stress state under triaxial conditions. The hydrate saturation of the samples was in the range of 50–90%. It was found that the initial effective water permeability was in range of 0.01 mD to tens of mD, depending on the hydrate saturation and the mean particle size of the host sediment. The hydrate pore space morphology is also a critical factor, and results suggest hydrates are forming in the pore centers of sand grains as pore filling, but also as a sediment grain coating. In a first for gas hydrate-bearing pressure cores, the permeability anisotropy was established via vertical and horizontal flow tests combined with a pore fluid flow simulation. The horizontal/vertical permeability ratio was found to be 4. Additionally, the effective stress dependency of permeability was investigated by performing flow tests at different effective stresses. Due to decreasing porosity and particle crushing, the permeability dropped by approximately 90% for an effective stress increase of 10 MPa.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Jang, J., Waite, W.F., Kumar, P., Tenma, N., 2019. Pressure core based onshore laboratory analysis on mechanical properties of hydrate-bearing sediments recovered during India's National Gas Hydrate Program Expedition (NGHP) 02. Marine and Petroleum Geology 108, 482-501.


A solid understanding of the mechanical properties of hydrate-bearing sediments is essential for the safe and economic development of methane hydrate as an energy resource. In 2015, 104 pressure cores were collected, recovering sediments from above and within concentrated hydrate reservoirs in the Krishna-Godavari Basin, as part of India's National Gas Hydrate Program Expedition 02 (NGHP-02). These cores provided minimally-disturbed sediment, retained at pressures and temperatures within the hydrate stability field, for the first-ever systematic triaxial test of dozens of subsections of hydrate-bearing pressure core sediments. Post-cruise testing in Japan evaluated multiple physical and hydro-mechanical properties. Consolidated drained and undrained triaxial compression tests, uniaxial (unconfined in effective stress) compression tests, multistage consolidation and compression tests, and alternating strain-rate compression tests were performed. Triaxial compression test results showed an increase in the strength and stiffness, as well as the positive dilatancy, with increasing hydrate saturation, supporting previous research on laboratory-formed and natural hydrate-bearing sediments. However, some strength results in this study were low compared to prior analyses of hydrate-bearing sediments. This low strength was likely caused by the host sediment's small particle size and loose packing, and the relatively slow applied compression strain rate. Results from uniaxial compression and multi-step compression tests confirmed that pore-space hydrates produce an apparent cohesion in hydrate-bearing sediment. More severe strength loss in sediments during the initial loading for multistage compression was also attributable to the presence of hydrates. The applicability of this multistage compression test for determining in situ properties was not confirmed, but results do provide bounds on the in situ values. Finally, from the variable strain-rate tests, it was revealed that strength in hydrate-bearing sediment has a large strain-rate dependence.

Yoneda, J., Oshima, M., Kida, M., Kato, A., Konno, Y., Jin, Y., Tenma, N., 2019. Consolidation and hardening behavior of hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin, offshore India. Marine and Petroleum Geology 108, 512-523.


Evaluating the consolidation properties and hardening behavior of reservoir with high concentrations of gas hydrate are crucial for the safe and development of gas hydrate as an energy resource. In addition, investigating the stiffness properties of the hydrate-bearing sediment promotes the prediction accuracy of hydrate content estimation from seismic survey and logging data. The hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin during India's National Gas Hydrate Program Expedition 02 were tested herein using a newly developed high-pressure oedometer chamber (HOC) and transparent acrylic cell triaxial testing (TACTT) system. The compression and swelling behavior of the sediments were observed by one-dimensional consolidation and isotropic loading and unloading compression tests using HOC and TACTT. Lateral earth pressure (at-rest stress) was measured using HOC, and compressional-wave (P) and shear (S) wave velocities were measured by TACTT under various stress conditions, including estimated in situ effective stress. The results revealed that the consolidation curve of the hydrate-bearing sediment is higher than that of the hydrate-free sediment. In the case of the normally consolidated state, the bulk volume of the hydrate-bearing sediment was compressed to the original consolidation curve of the hydrate-free sediment after hydrate dissociation. However, when the sediment experienced over-consolidation, it did not compress owing to the hydrate dissociation. In addition, the K0 value of the hydrate-bearing sediment was greater than the hydrate-free sediment and exhibited a larger hysteresis during loading and unloading. The isotropic loading and unloading tests confirmed that hydrate existence hardened the compression and swelling indexes. Based on the P and S wave velocities, the morphology of hydrate in the sediment in situ was assumed to be of a load-bearing type. An empirical equation was then proposed to estimate the shear modulus using the relation between S wave velocity, hydrate saturation, and effective confining pressure.

Yonkofski, C., Tartakovsky, G., Huerta, N., Wentworth, A., 2019. Risk-based monitoring designs for detecting CO2 leakage through abandoned wellbores: An application of NRAP’s WLAT and DREAM tools. International Journal of Greenhouse Gas Control 91, 102807.


As geologic CO2 storage (GCS) moves towards industrial-scale deployment, strategies must be developed to ensure long-term environmental risks related to potential leakage are managed. One approach to is to perform risk-based subsurface monitoring targeting early leak detection. Early detection is particularly important to address the risk associated with leakage along legacy wells. The challenge in risk-based monitoring is that leakage impacts are expected to be small in comparison with the footprint of the stored CO2 plume and could occur over considerable depths, ranging from the storage formation up to surficial aquifers. Here we demonstrate the application workflow of two of the National Risk Assessment Partnership’s (NRAP) computational tools, WLAT (Wellbore Leakage Analysis Tool) and DREAM (Designs for Risk Evaluation and Management), to a hypothetical CO2 storage site based on a study area in the Midwestern United States. By incorporating site specific wellbore integrity analyses, results show how fluid leakage may be estimated, evaluated, and monitored in terms of risk. For the selected site, three monitoring wells were ultimately needed to detect all possible CO2 leaks and six monitoring wells were needed to minimize time to leak detection. Such analyses inform stakeholders about long-term liability and monitoring costs of GCS projects.

Yu, T.-T., Wang, B., Jarzembowski, E., 2019. First record of marine gastropods (wentletraps) from mid-Cretaceous Burmese amber. Palaeoworld 28, 508-513.


Gastropod fossils are rarely preserved in amber with only a few records of terrestrial snails. Two new species, Epitonium (Epitonium) zhuoi n. sp. and Epitonium (Papyriscala) lyui n. sp. are described based on two well-preserved specimens from mid-Cretaceous amber from northern Myanmar. Highresolution three-dimensional images using X-ray micro-computed tomography (micro-CT) are provided. These species can be attributed to the family Epitoniidae (wentletraps) based on the shell characters such as the slender and conical shell-shape, numerous whorls, round aperture and regular, axial sculpture of high, sharply-ribbed costae. Our find is the first

record of marine gastropods preserved in amber, and suggests that the Burmese amber forest probably existed close to the seashore.

Yue, P., Cui, X., Wu, W., Gong, Y., Li, K., Goulding, K., Liu, X., 2019. Impacts of precipitation, warming and nitrogen deposition on methane uptake in a temperate desert. Biogeochemistry 146, 17-29.

https://doi.org/10.1007/s10533-019-00606-0

Desert soils are a significant global sink for methane (CH4). However, it remains unclear how CH4 uptake in temperate deserts could respond to elevated precipitation, nitrogen (N) deposition and warming. An in situ field experiment was conducted to investigate these effects on CH4 uptake in the Gurbantunggut Desert, northwest China, from September 2014 to August 2017. This desert was a weak sink for CH4 (0.83 kg C ha−1 year−1) over this period, with the non-growing season (November–March) accounting for 30.5% of the annual CH4 uptake. Pulse CH4 uptake was found to result from increased water addition (by 30% or 60 mm year−1) and low N deposition (30 kg N ha−1 year−1) which enhanced annual CH4 uptake by 62.3 and 52.6%, respectively. However, no significant impact of high N deposition (60 kg N ha−1 year−1) was found. Warming in open topped chambers (OTCs) had a variable effect on CH4 uptake, which mainly depended on variation in soil moisture. The response in CH4 uptake to the interaction between water and N addition was less than that for the individual factors, except under conditions of warming. In addition, CH4 uptake was significantly positively correlated to water-filled pore space (WFPS), differing from observations in forest and grassland ecosystems. Structural equation modeling indicated that CH4 uptake was significantly enhanced by soil moisture and the underground biomass of ephemerals. Overall, the CH4 sink of this desert was significantly enhanced by increasing precipitation and low N deposition, rather than warming, which may become a feedback for future climate.

Zaitsu, K., Noda, S., Ohara, T., Murata, T., Funatsu, S., Ogata, K., Ishii, A., Iguchi, A., 2019. Optimal inter-batch normalization method for GC/MS/MS-based targeted metabolomics with special attention to centrifugal concentration. Analytical and Bioanalytical Chemistry 411, 6983-6994.

https://doi.org/10.1007/s00216-019-02073-w

This study investigated the optimal inter-batch normalization method for gas chromatography/tandem mass spectrometry (GC/MS/MS)-based targeted metabolome analysis of rodent blood samples. The effect of centrifugal concentration on inter-batch variation was also investigated. Six serum samples prepared from a mouse and 2 quality control (QC) samples from pooled mouse serum were assigned to each batch, and the 3 batches were analyzed by GC/MS/MS at different days. The following inter-batch normalization methods were applied to metabolome data: QC-based methods with quadratic (QUAD)- or cubic spline (CS)-fitting, total signal intensity (TI)-based method, median signal intensity (MI)-based method, and isotope labeled internal standard (IS)-based method. We revealed that centrifugal concentration was a critical factor to cause inter-batch variation. Unexpectedly, neither the QC-based normalization methods nor the IS-based method was able to normalize inter-batch variation, though MI- or TI-based normalization methods were effective in normalizing inter-batch variation. For further validation, 6 disease model rat and 6 control rat plasma were evenly divided into 3 batches, and analyzed as different batches. Same as the results above, MI- or TI-based methods were able to normalize inter-batch variation. In particular, the data normalized by TI-based method showed similar metabolic profiles obtained from their intra-batch analysis. In conclusion, the TI-based normalization method is the most effective to normalize inter-batch variation for GC/MS/MS-based metabolome analysis.

Zangrando, R., Zanella, V., Karroca, O., Barbaro, E., Kehrwald, N.M., Battistel, D., Morabito, E., Gambaro, A., Barbante, C., 2020. Dissolved organic matter in the deep TALDICE ice core: A nano-UPLC-nano-ESI-HRMS method. Science of The Total Environment 700, 134432.


Trace organic compounds in deep ice cores supply important paleoclimatic information. Untargeted analyses of dissolved organic matter provide an overview of molecular species in ice samples however, sample volumes

usually required for these analyses are generally not available from deep ice cores. Here, we developed an analytical method using a nano-UPLC-nano-ESI-HRMS to detect major molecular species in ice cores. Samples (4 µL) from the TALos Dome Ice CorE (TALDICE), allowed investigating molecular species across a range of depths including during glacial and interglacial periods. We detected 317 chemical species that were tentatively assigned to fatty acids, hydroxy fatty acids and their degradation products (oxo-fatty acids and dicarboxylic acids), as well as oxidation byproducts of isoprene and monoterpenes. These compounds indicate that the main sources of the organic fraction are microbes as well as primary and secondary aerosols. Interglacial samples encompass a wide range of species including compounds from the oxidation of isoprene and monoterpenes as well as unsaturated fatty acids, while the glacial samples contained less diverse species. This difference may be due to decreased temperatures during the glacial period inhibiting terrestrial vegetation growth and increasing the sea ice extent, thereby weakening the emission sources.

Zeng, F., Peng, F., Guo, J., Rui, Z., Xiang, J., 2019. Gas mass transport model for microfractures considering the dynamic variation of width in shale reservoirs. SPE Reservoir Evaluation & Engineering 22, 1265-1281.

https://doi.org/10.2118/194494-PA

Microfractures are commonly observed in shale reservoirs. During the shale gas-production process, stress sensitivity induces a change in the width of the microfractures, which is a significant factor that affects shale gas mass transport. By using research methods based on desorption theory and elastic-plastic mechanics, a shale gas mass transport model that considers the dynamic variations in the microfracture width is established in this paper. This model comprehensively fuses the surface diffusion model, slip flow model, Knudsen diffusion model, and cubic grid model. The reliability of this model is verified using molecular simulations, which do not include surface diffusion. The shale gas is considered as pure methane. Then, the different contributions of the gas mass transport mechanisms to the total mass transport are discussed in detail. The results demonstrate the following findings: (1) The studied flows are well-simulated by the proposed model. (2) Stress sensitivity results in a decrease in gas mass transport when the formation pressure exceeds 3.4 MPa, and the minimum value is approximately 0.45 times smaller than that when the width change is not considered. Moreover, stress sensitivity results in an increase in gas mass transport when the formation pressure is lower than 3.4 MPa, and the maximum value is approximately 4.5 times higher than that when the width change is not considered. (3) Shale gas mass transport is positively associated with the Young’s modulus and Poisson’s ratio, whereas it is negatively associated with the microfracture compressibility. When the formation pressure is less than 4 MPa, shale gas transport is positively correlated with the desorption capacity, whereas when the formation pressure exceeds 4 MPa, the effect of different desorption capacities on gas transport is nearly consistent. (4) When the microfracture width is at nanoscale and the reservoir pressure is lower than 15 MPa, surface diffusion has an obvious effect on the shale gas mass transport process. When the contribution of surface diffusion to the total shale gas mass transport is relatively small, the contributions of slip flow and Knudsen flow to shale gas mass transport exhibit the trend of “shifting each other.” When the surface diffusion contribution is larger, a reduction in its contribution leads to simultaneous initial increases in the contributions of slip flow and Knudsen flow to shale gas mass transport, and then these flows begin “shifting each other.”



Significance: Archaea synthesize distinctive membrane-spanning lipids (GDGTs) that are readily preserved in ancient sediments and utilized as paleotemperature proxies to reconstruct sea surface temperatures deep in Earth’s past. However, properly interpreting GDGT-based biomarker proxies requires an accurate assessment of the archaea that contribute to GDGT pools in modern environments and of the proteins necessary for synthesizing GDGTs. In this study, we identify 2 radical SAM proteins in Sulfolobus acidocaldarius that are required to produce these molecules. Bioinformatics analyses of these GDGT ring synthesis proteins reveal that

Thaumarchaeota are the dominant source of cyclized GDGTs in the open ocean, allowing us to constrain one factor of uncertainty in the application of GDGT-based paleotemperature proxies.

Abstract: Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are distinctive archaeal membrane-spanning lipids with up to eight cyclopentane rings and/or one cyclohexane ring. The number of rings added to the GDGT core structure can vary as a function of environmental conditions, such as changes in growth temperature. This physiological response enables cyclic GDGTs preserved in sediments to be employed as proxies for reconstructing past global and regional temperatures and to provide fundamental insights into ancient climate variability. Yet, confidence in GDGT-based paleotemperature proxies is hindered by uncertainty concerning the archaeal communities contributing to GDGT pools in modern environments and ambiguity in the environmental and physiological factors that affect GDGT cyclization in extant archaea. To properly constrain these uncertainties, a comprehensive understanding of GDGT biosynthesis is required. Here, we identify 2 GDGT ring synthases, GrsA and GrsB, essential for GDGT ring formation in Sulfolobus acidocaldarius. Both proteins are radical S-adenosylmethionine proteins, indicating that GDGT cyclization occurs through a free radical mechanism. In addition, we demonstrate that GrsA introduces rings specifically at the C-7 position of the core GDGT lipid, while GrsB cyclizes at the C-3 position, suggesting that cyclization patterns are differentially controlled by 2 separate enzymes and potentially influenced by distinct environmental factors. Finally, phylogenetic analyses of the Grs proteins reveal that marine Thaumarchaeota, and not Euryarchaeota, are the dominant source of cyclized GDGTs in open ocean settings, addressing a major source of uncertainty in GDGT-based paleotemperature proxy applications.

Zhang, B., Kang, J., Kang, T., Kang, G., Zhao, G., 2019. Molecular dynamics simulations of CH4 diffusion in kaolinite: influence of water content. International Journal of Coal Science & Technology 6, 556-563.

https://doi.org/10.1007/s40789-019-00275-2

Understanding the interaction of CH4 with kaolinite is significant for researchers in the fields of coalbed CH4 and shale gas. The diffusion behaviors of CH4 in kaolinite with water contents ranging from 0 to 5 wt% have been analyzed by molecular dynamics simulations. The results of the simulations indicate that CH4 molecules can jump between adjacent holes in the kaolinite matrix. CH4 diffusion coefficient was very low (3.28 × 10−9 m2/s) and increased linearly with the increasing of water content. As the water content decreased, the value of radial distribution function first peak between CH4 and oxygen was larger, meaning that with lower water content, the interaction energy between CH4 and oxygen in kaolinite is stronger. The interaction between CH4 and water is linearly positively correlated with water content, in contrast, the interaction energy between kaolinite and water as well as between kaolinite and CH4 decreased linearly with increasing water content. On the other hand, the diffusion of CH4 molecules adsorbed on the surfaces also can be accelerated by the fast diffusion of water molecules in the middle micropore of the kaolinite.

Zhang, B., Yao, S., Mills, B.J.W., Wignall, P.B., Hu, W., Liu, B., Ren, Y., Li, L., Shi, G., 2020. Middle Permian organic carbon isotope stratigraphy and the origin of the Kamura Event. Gondwana Research 79, 217-232.


Large carbon cycle perturbations associated with the Middle Permian (Capitanian) mass extinction have been widely reported, but their causes and timing are still in dispute. Low resolution carbon isotope records prior to this event also limit the construction of a Middle Permian chemostratigraphic framework and global or local stratigraphic correlation, and hence limit our understanding of carbon cycle and environmental changes. To investigate these issues, we analyzed the 13Corg values from the Middle Permian chert-mudstone sequence (Gufeng Formation) in the Lower Yangtze deep-water basin (South China) and compared them with published records to build a chemostratigraphic scheme and discuss the underlying environmental events. The records show increased δ13Corg values from late Kungurian to early Guadalupian, followed by a decrease to the late Wordian/early Capitanian. The early-mid Capitanian was characterized by elevated δ13Corg values suggesting the presence of the “Kamura Event”: an interval of heavy positive values seen in the δ13Ccarb record. We propose that these heavy Capitanian δ13C values may be a response to a marked decline in chemical weathering rates on Pangea and associated reduction in carbonate burial, which we show using a biogeochemical model. The

subsequent negative δ13C excursion seen in some carbonate records, especially in shallower-water sections (and in a muted expression in organic carbon) coincide with the Capitanian mass extinction may be caused by the input of isotopically-light carbon sourced from the terrestrial decomposition of organic matter.

Zhang, J., Cao, J., Xiang, B., Zhou, N., Ma, W., Li, E., 2019. Fourier-transform infrared proxies for oil source and maturity: Insights from the early Permian alkaline lacustrine system, Junggar Basin (NW China). Energy & Fuels 33, 10704-10717.


Fourier-transform infrared (FTIR) spectroscopy has been widely applied in oil geochemical studies, particularly with respect to the physical properties and maturity of hydrocarbons. However, in general, it has been seldom used to investigate the organic matter (OM) depositional environment and source of oil. In this paper, we present such an FTIR spectroscopy study based on a case investigation in the early Permian alkaline–lacustrine-derived oils from the Mahu sag, Junggar Basin, Northwest China. The results define 13 FTIR structural parameters that are associated with the OM depositional environment, source, and maturity of oil based on a comparison with well-established oil carbon isotopic and biomarker data. These would be general to the alkaline (saline)–lacustrine petroleum systems worldwide. Further combined FTIR spectroscopy and biomarker parameters in the study area reveal that the lower Permian Fengcheng formation-derived oils in the Mahu sag were generated from source rocks deposited in alkaline–saline to brackish–freshwater environments. The oils have a zoned occurrence, reflecting the general rules of hydrocarbon generation in alkaline lacustrine environments. This study represents the first FTIR spectroscopy study of alkaline–lacustrine oils and suggests that FTIR spectroscopy appears to have considerable potential in advancing oil geochemical research. The data demonstrate potential for guiding regional oil exploration.

Zhang, J., Yu, Z., Jia, G., 2020. Cyclisation degree of tetramethylated brGDGTs in marine environments and its implication for source identification. Global and Planetary Change 184, 103043.


Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are ubiquitous in marine environments. Nevertheless, it is unclear whether these brGDGTs are derived from terrestrial soils or produced in situ. Recently, it was proposed that the weighted average number of cyclopentane moieties of tetramethylated brGDGTs, #Ringstetra, could be used to identify sources of sedimentary brGDGTs in marine environments. However, little is known about #Ringstetra in seawater. In this study, we report #Ringstetra data in suspended particulate materials (SPM) in the surface shelf waters of the East China Sea (ECS) and coastal South China Sea (SCS), as well as in core-top sediments of the deep SCS. According to a two-end member model, #Ringstetra values in SPM increase offshore from 0.48 to 0.86 in the ECS and from 0.39 to 0.83 in the SCS, suggesting increasing marine-produced brGDGTs. An offshore increasing trend of #Ringstetra is also observed in the shelf surface sediments of the ECS and SCS, suggesting increased contributions of marine-produced brGDGTs. However, the offshore increasing trend in core-top sediments of the SCS ceases at a water depth ca. 100 m, with constantly low #Ringstetra values (0.3 ± 0.1) at sites deeper than 780 m and a transition value of 0.58 at 329 m. Instead of interpreting the low #Ringstetra values in deep-sea sediments as the result of increased contributions of terrestrial-derived brGDGTs, we propose that brGDGTs in deep-sea sediments are produced in situ. The lower pH in the deep-sea bottom water and sediment porewater than in the seawater column could be the reason for the low #Ringstetra values. We further propose that pH reconstructions of deep-sea sediment cores (e.g., >1000 m water depth) with the least terrestrial influence should reflect pH changes in marine bottom environments.



Tectonic deformation acts as an indispensable factor affecting the crystalline structure, but its relationship with the evolution mechanism of the morphological structure is seldom considered. In this work, the characterization of microcrystalline and morphological structures in tectonic coal was comprehensively explored using X-ray diffraction (XRD), pore structure analyzers (liquid nitrogen and mercury intrusion methods), and micro-computed tomography (micro-CT). The XRD results indicate that a transformation of the chemical composition was observed in the coal body after continuous tectonic deformation. Meanwhile, the variation in microcrystalline parameters, such as the interlayer spacing (d002), stacking height (Lc), effective stacking layer number (Nave), aromaticity (fa), and graphitization degree (g), reveal that the microcrystalline structure of tectonic coal has experienced a positive evolution with graphitization and aromatization. Pore morphological analyses demonstrate that pore volume distributions of micropores, mesopores, and macropores were totally enhanced by tectonism while the pore shape potentially changes slightly. Simultaneously, the incremental noneffective pores of tectonic coal may promote gas accumulation and storage in the pore space. Fracture morphological analyses utilizing micro-CT lay emphasis on the orderly distributed cleats with a uniform scale in original coal, whereas the reconstruction of microstructures in tectonic coal illustrates a scattered distribution with good connectivity. In addition, the evolution of the macromolecular structure has an influence on the growth of nanoscale pores since the lattice defects may generate from the interlayer of the aromatic ring or the internal space. This research is of an enlightening significance for understanding the influence of tectonic stress on the chemical structure evolution of coals and its relationship with the nanoscale morphological structure development in tectonic coal.

Zhang, M.-h., Qiao, J.-h., Zhao, G.-x., Lan, X.-y., 2019. Regional gravity survey and application in oil and gas exploration in China. China Geology 2, 382-390.


ABSTRACT Ground gravity survey for regional structure unit delineation and oil and gas exploration in China is addressed in this paper with examples. Gravity survey scales, coverage, technical regulations and achievements at the national level are introduced, including data processing and anomaly interpretation techniques. Bouguer anomalies of terrestrial territories of China and classification of anomalous feature zones are also described; they are well correlated with lithotectonical boundaries, fault zones, and unexposed igneous plutons. Recent study results of petroliferous sedimentary basins are presented as well, including concealed boundaries and major structures of large basins. It is concluded that gravity survey is the most effective and economic method in unveiling unexposed and deep-seated structures, targeting and delineating oil and gas-bearing sedimentary basins, and locating main trap structures within prolific basins in early stage of exploration in China. Suggestions for improving exploration of both conventional and unconventional oil and gas reservoirs in China are also given in the paper.

Zhang, M., Li, Z., 2019. Biodegradation characteristics of oil shale in the Permian Lucaogou Formation in the southeast of the Junggar Basin, China: implications from organic geochemistry. Oil Shale 36, 501–513.

https://doi.org/10.3176/oil.2019.4.04

The Permian Lucaogou Formation oil shale in the southeast of the Junggar Basin is the oldest oil shale in China. In this study, the biodegradation characteristics of the oil shale are investigated based on organic geochemistry. The analytical results show that the biodegraded oil shale contains large humps of unresolved complex mixtures (UCMs) and is depleted of n-alkanes and acyclic isoprenoids (pristine (Pr), phytane (Ph), iC18, iC17, iC16, iC15 and iC14). Furthermore, C14–C16 bicyclic terpanes are completely preserved. It can be concluded that the biodegradation level of the Lucaogou Formation oil shale is PM1–PM2. In addition, the values of aromatic hydrocarbon proxies (methyldibenzothiophene/dibenzothiophene (MDBT/DBT), dimethyldibenzothiophene/methyldibenzothiophene (DMDBT/MDBT), 1,2,7-trimethylnaphthalene/1,3,6-trimethylnaphthalene (1,2,7-TMN/1,3,6-TMN) and 1,2,4-trimethylnaphthalene/1,6,7-trimethylnaphthalene (1,2,4-TMN/1,6,7-TMN)) also reflect a low bio-degradation level. The well-preserved TMN derivatives indicate that the biodegradation level of the Lucaogou Formation oil shale is below PM3.



In carbonate isotopic measurements, H2O2 treatment is one of the most often used methods to remove organic matter contaminants from carbonate minerals for accurate analysis, but the interaction between H2O2 solution and carbonate minerals may also lead to analytical bias. In this study, we quantitatively tested the effect of H2O2

treatment for 7 types of carbonate minerals, and the influences on Δ47 values of calcium carbonate are systematically discussed for the first time. Most samples presented Δ47 offsets within the 2-SD of our analytical precision, except the methane derived authigenic carbonate (MDAC). The shift of Δ47 values in MDACs is attributed to the mixing effect of two types of carbonate minerals: original one and isotopically altered one, and the magnitude is determined by the differences of both δ13C and δ18O values between two endmembers. Regarding biogenic carbonate tested here, the analytical bias of H2O2 treatment is relative small in δ13C and δ18O values, and therefore the shift of Δ47 values is statistically neglectable.

The δ13C and δ18O values for most samples tested in this study became positive (up to +1.7‰) after H2O2 treatment. Apart from previously well discussed mechanisms, such as removal of organic contamination, isotopic fractionation during the partial dissolution and dissolution of isotopic distinct carbonate compositions in the heterogeneous minerals, we experimentally demonstrated carbon and oxygen isotopic exchanges between carbonate minerals and H2O2 solution for the first time. The δ13C and δ18O values of carbonate were influenced by isotopic exchanges with atmospheric CO2 in the CO2-HCO3

−-CO32− system and H2O in H2O2 solution,

respectively. Rich transition metals in the authigenic carbonate minerals (e.g. MDAC, travertine), which catalyze H2O2 decomposition, can enlarge this effect by altering H2O isotopic compositions. Though the small shift of δ13C and δ18O in biogenic carbonate observed here (up to 0.6‰) would not change scientific interpretations and conclusions in most of previous studies, cautions should be taken in the future.

Based upon our new experimental results, we suggest using a buffered H2O2 solution (pH≈8) isolated from atmospheric CO2 to remove potential organic contaminations in biogenic carbonate. For authigenic carbonate, H2O2 treatment is not recommended. If necessary, decreasing the H2O2 concentration, shortening the reaction time, leaving the solution in a CO2-free environment, and adjusting the solution to a basic condition will improve the accuracy in isotopic analysis of these minerals.



For many years, the Yangtze Platform has been successfully explored and exploited for petroleum. The Lower Silurian Longmaxi Shale proved to contain commercial quantities of gas, but several other formations might also have a high potential for shale-hosted gas exploration. This paper comprises of geochemical, petrographical, petrophysical and mineralogical information on the major Proterozoic and Paleozoic gas shales in the Upper Yangtze area, which provides insights on the depositional environment, the thermal maturity of organic matter, shale gas storage capacity and the fracability of these rocks. The total organic carbon (TOC) content varies from 0.1 to 22.5% with an average value of 2.7% and most of these shales were deposited in an oxygen-depleted marine environment. Equivalent vitrinite reflectance (VRr) values range from 2.20 to 4.25%, indicating that all samples are in the gas generation window and lost a large amount of primary organic carbon. Porosity varies between 1.5 and 13.6% with an average value of 5.8%, while the excess sorption capacity ranges from 0.10 to 0.22 mmol/g rock. Minerology data show that quartz is the predominant mineral except for the Upper Permian Longtan Formation, in which clay minerals account for 29 to 84%. New data were combined with those from other publications and compared to information on other, well-studied shale-hosted gas systems.


https://doi.org/10.1002/gj.3351

A comprehensive analysis on high-resolution seismic data and the geological characteristics of the Qiongdongnan Basin (QDNB) in the northern South China Sea reveals multiple seismic evidence indicative of hydrocarbon migration and gas hydrate accumulation, including mud diapirs, gas chimneys, bottom simulating reflectors (BSRs), acoustic blanking, enhanced reflections, V-AMP structures, elevated stacking velocity of sediments, and seafloor expressions. Mud diapirs and gas chimneys, which are characterized by acoustic turbidity, fuzziness, and blanking reflections on seismic profiles, with a diversity of structures and scales, are widespread and concentrated in the centres of sags and the transitional zones between sags and uplifts. Five BSR regions, with a total area of approximately 11,000 km2, have been delineated in the QDNB. They have high or medium-high continuity amplitudes with overlying acoustic blanking on seismic profiles, indicating the occurrence of gas hydrate. Distinct fluid seepage phenomena are common below the BSRs, demonstrating that abundant free gas has migrated and accumulated beneath the gas hydrate. The distribution of BSRs and the developed zones of mud diapirs and gas chimneys presents a spatial superposition feature, and the BSRs are usually located on top of or within the structural highs of the mud diapirs and gas chimneys, indicating a close relationship between them. Mud diapirs, gas chimneys, and associated faults are efficient pathways for migrating hydrocarbons, through which the mature to highly mature thermogenic gas of the Palaeogene strata and the biogenic gas of the Neogene sediments migrate to the gas hydrate stability zones and form gas hydrate. Gas hydrate samples were recovered from the gas chimney area during the remote operated vehicle (ROV) investigation in deepwater QDNB in 2015. Based on the seismic interpretation and geochemical results, we propose two models of gas hydrate accumulation in the deepwater area of the QDNB: (a) near source biogenic gas hydrate with self-generation and self-accumulation, and (b) distal source thermogenic gas hydrate with lower generation and upper accumulation. We believe that the areas with a fine spatial coupling configuration between the mud diapirs, gas chimneys, and BSRs are favourable exploration targets for gas hydrate in the QDNB.

Zhang, Y., Huang, S., Sheng, J.J., Jiang, Q., 2020. Experimental and analytical study of oxygen consumption during air injection in shale oil reservoirs. Fuel 262, 116462.


AIP (air injection process) is applied as an EOR (Enhanced oil recovery) method in conventional oil reservoirs, while the implementation of AIP in shale oil reservoirs has rarely been studied. The thermal effect of AIP in shale oil reservoirs is insignificant considering its low air injectivity, and the main challenge is whether the produced oxygen concentration at the production well can be reduced below 10% to avoid the potential safety hazards. In this paper, an analytical method was proposed to estimate the produced oxygen concentration during AIP, where the oxygen reaction rate was measured by the SBR (small batch reactor) experiments. In the SBR tests, a constant oxygen reaction rate was observed at a corresponding reservoir temperature. A higher reservoir temperature resulted with greater oxygen consumption. The air flooding tests were conducted with shale core and the proposed analytical method was validated by the air flooding tests. The analytical method was further applied to investigate the AIP feasibility in the air flooding tests. The results indicate that a core needs to be a longer than 0.132 m, or the injection pressure is lower than 2.68E + 06 Pa (388.70 psi), to satisfy the produced oxygen concentration requirement for AIP. This study can explore the potential of air injection in developing shale oil reservoirs and provide insights to the AIP projects in field level.

Zhang, Y., Muxworthy, A.R., Jia, D., Wei, G., Xia, B., Wen, B., Wang, M., Liu, W., Brzozowski, M.J., 2019. Identifying and dating the destruction of hydrocarbon reservoirs using secondary chemical remanent magnetization. Geophysical Research Letters 46, 11100-11108.

https://doi.org/10.1029/2019GL084812

Destructive processes are thought to be common in pre-Cenozoic oil-gas reservoirs. The timing, mechanism, and even identification of these processes, however, are difficult to clearly characterize, which obscures the evolution of such systems and the assessment of oil and gas reserves. Here, we reveal a new link between secondary chemical remanent magnetization acquisition and tectonically driven destruction of hydrocarbon reservoirs, which can be used to date the destructive processes and identify their tectonic controls. We performed a detailed paleomagnetic analysis of rocks from a typical destroyed reservoir (Majiang reservoir, China) and combined these data with scanning electronic microscope imaging and strontium isotope, total organic carbon, and clay analysis. We found that the Late Triassic syntilting secondary chemical remanent magnetizations of source and reservoir rocks resulted from the destructive processes driven by the Indosinian orogeny. We therefore argue that palaeomagnetic methods can be used to constrain destructive events within hydrocarbon reservoirs worldwide.

Zhang, Z., Wang, C., Lv, D., Hay, W.W., Wang, T., Cao, S., 2020. Precession-scale climate forcing of peatland wildfires during the early middle Jurassic greenhouse period. Global and Planetary Change 184, 103051.


As an important terrestrial carbon reservoir, peatland has the potential to influence the global carbon cycle and global climate. In recent decades, the frequency and extent of peatland wildfires in boreal and tropical regions are increasing owing to climate change and human activity. However, the processes that govern changes in peatland wildfire are poorly understood over long timescales, particularly on the orbital scales. We analyzed coal petrology and geochemistry in coal seams of the Aalenian Yan'an Formation in Ordos Basin to identify peatland wildfire records based on the co-occurrence of charcoal and pyrolytic polycyclic aromatic hydrocarbons (PAHs). In addition, the presence of widespread peatland wildfires has suggested that atmospheric oxygen concentration at the time should be substantially higher than the minimum needed for sustained combustion. Spectral analysis of vitrinite/inertinite (V/I) and inertinite reflectance data demonstrate that peatland wildfires were controlled by precession cycles owing to a shift in the seasonal contrast and amount of rainfall. Our results provide essential context for understanding the importance of peatland wildfires carbon emissions in a coupling of orbital forcing, climate, and the carbon cycle.


https://doi.org/10.1038/s41598-019-51515-z

Although tropical forest soils contributed substantially global soil methane uptake, observations on soil methane fluxes in tropical forests are still sparse, especially in Southeast Asia, leading to large uncertainty in the estimation of global soil methane uptake. Here, we conducted two-year (from Sep, 2016 to Sep, 2018) measurements of soil methane fluxes in a lowland tropical forest site in Hainan island, China. At this tropical forest site, soils were substantial methane sink, and average annual soil methane uptake was estimated at 2.00 kg CH4-C ha−1 yr−1. The seasonality of soil methane uptake showed strong methane uptake in the dry season (−1.00 nmol m−2 s−1) and almost neutral or weak soil methane uptake in the wet season (−0.24 nmol m−2 s−1). The peak soil methane uptake rate was observed as −1.43 nmol m−2 s−1 in February, 2018, the driest and coolest month during the past 24 months. Soil moisture was the dominant controller of methane fluxes, and could explain 94% seasonal variation of soil methane fluxes. Soil temperature could not enhance the explanation of seasonal variation of soil methane fluxes on the top of soil moisture. A positive relationship between soil methane uptake and soil respiration was also detected, which might indicate co-variation in activities of methanotroph and roots and/or microbes for soil heterotrophic respiration. Our study highlights that tropical forests in this region acted as a methane sink.

Zhao, X., Pu, X., Zhou, L., Jin, F., Shi, Z., Han, W., Jiang, W., Zhang, W., 2020. Typical geological characteristics and exploration practices of lacustrine shale oil: A case study of the Kong-2 member strata of the Cangdong Sag in the Bohai Bay Basin. Marine and Petroleum Geology 113, 103999.


Successful development of marine shale oil in North America has advanced the researches on lacustrine shale oil in China. However, there remains no unified understanding of certain issues, such as the exploration prospects of lacustrine shale oil. To determine the typical geological characteristics and exploration potential of lacustrine shale oil in China, the shale strata of the Kong-2 Member in the Cangdong sag was selected as a study system. The geologic setting, characteristics, and distribution of sweet spots, as well as the exploration prospects of lacustrine shale oil were analyzed using 635.8 m cores and the analytical data for 12,000 core samples from three wells,G108-8, GD12, and GD14; oil testing and production testing data from multiple wells were also evaluated. Results show that the shale oil developed in a slightly reductive and tectonically stable sedimentary environment. The shale strata are composed of various minerals, including mainly quartz, feldspar, and dolomite, with abundant laminae. Samples with total organic carbon (TOC) values > 1% account for>75% of the shales, which are primarily type I and type II-1 kerogen with thermal maturities between 0.5% and 1.1%, and formed during the oil window. These lacustrine shales have multiple types of reservoir spaces, including organic pores, intercrystalline pores, intergranular pores, microfractures, and laminar fractures, with an average (all averages are arithmetic means) OSI index (pyrolysis S1 × 100/TOC)of 147.1 mg oil/g TOC, and an average brittleness index >50. The reexamination of old wells and horizontal well exploration aimed at the sweet spots of type Ia and Ib oils have achieved promising results. Well KN9 had a daily oil production of 29.6 m3 after fracturing, and horizontal well GD1701H exhibited its highest daily oil production at 75.9 m3, and currently produces 21–24m3consistently. Well GD1702H had a maximum daily oil production of 61 m3, and stably produces 20–25 m3 at present. The resources of the Ek2

1SQ⑨ sequence calculated using amass oil content method were 208 million tons, confirming the extensive exploration potential of shale oil in this lacustrine lake basin.

Zhao, Y., Wang, L., Luo, J., Huang, T., Tao, S., Liu, J., Yu, Y., Huang, Y., Liu, X., Ma, J., 2019. Deep learning prediction of polycyclic aromatic hydrocarbons in the high Arctic. Environmental Science & Technology 53, 13238-13245.


Given the lack of understanding of the complex physiochemical and environmental processes of persistent organic pollutants (POPs) in the Arctic and around the globe, atmospheric models often yield large errors in the predicted atmospheric concentrations of POPs. Here, we developed a recurrent neural network (RNN) method based on nonparametric deep learning algorithms. The RNN model was implemented to predict monthly air concentrations of polycyclic aromatic hydrocarbons (PAHs) at the high Arctic monitoring station Alert. To train the RNN system, we used MODIS satellite remotely sensed forest fire data, air emissions, meteorological data, sea ice cover area, and sampled PAH concentration data from 1996 to 2012. The system was applied to forecast monthly PAH concentrations from 2012 to 2014 at the Alert station. The results were compared with monitored PAHs and an atmospheric transport model (CanMETOP) for POPs. We show that the RNN significantly improved PHE and BaP predictions from 2012 to 2014 by 62.5 and 91.1%, respectively, compared to CanMETOP predictions. The sensitivity analysis using the Shapley value reveals that air emissions determined the magnitude of PAH levels in the high Arctic, whereas forest fires played a significant role in the changes in PAH concentrations in the high Arctic, followed by air temperature and meridional wind fields.

Zhong, T., Liao, P., Chen, Q.-x., Li, N., Deng, H.-c., Liu, Q.-j., Luo, Y.-l., Lan, H.-x., Li, C.-y., 2019. Imaging the pore structure in geomaterials using rhodamine B covalently decorated magnetic nanoparticles. ACS Earth and Space Chemistry 3, 2482-2489.


There has been a recent booming development of multifunctional nanoparticles with precisely defined materials and an accompanying abundance of synthesis methods. However, developing a rational strategy to choose the proper nanoparticle and optimal synthesis method for geological applications remains a bottleneck. Here, a rhodamine B covalently decorated Fe3O4 nanoparticle was studied to assess its application as a novel

bifunctional nanomarker for the optical imaging of the pore structure in geomaterials. With this bifunctional nanomarker, we were able to combine magnetic injection, which provides a simple and non-destructive way of introducing the nanomarker into rocks, with fluorescence imaging techniques, which provide clear contrast imaging between geomaterials (black) and porosity (bright). The covalent bifunctional nanomarker exhibits higher fluorescence and less leakage of the fluorescence dye than those produced by the physical coating method. It offers not only a more practical and reliable nanomarker for the analysis of the pore structure in geomaterials but also contributes to nanomaterial-oriented research for various geological applications.



Dissolved organic matter (DOM) released from permafrost thaw greatly influences the biogeochemical cycles of, among others, downstream carbon, nitrogen and phosphorus cycles; yet, knowledge of the linkages between bacterial communities with permafrost DOM heterogeneity is limited. Here, we aim at unravelling the responses of bacterial diversities and metabolic profiles to DOM quantity and composition across permafrost thawing gradients by coupling an extensive field investigation with bio-incubation experiments. Richness, evenness and dissimilarities of the whole and rare communities decreased from thermokarst pits to headstreams and to downstream rivers. The assemblages of the abundant subcommunities were mainly determined by ecological drift-driven stochastic processes. Both the optical and the molecular composition of DOM were significantly related to the changes of the whole (rare) bacterial communities (Mantel’s correlation > 0.5, p < 0.01). Diversity indices of the whole and rare communities decreased with decreasing relative abundance of tannins, condensed aromatics and more aromatic and oxidized lignins as well as with decreased dissolved organic carbon and intensities of all fluorescence components. Laboratory DOM bio-incubation experiments further confirmed microbial consumption of more aromatic and oxidized compounds as well as decreasing metabolic diversities in terms of microbial degradation and production along permafrost thawing gradients. Our findings suggest that changes in the sources of permafrost-derived DOM induced by global warming can have different influences on the diversity and metabolism of bacterial communities and thus on permafrost carbon climate feedbacks along permafrost thawing gradients.

Zhou, Y., Zhou, L., He, X., Jang, K.-S., Yao, X., Hu, Y., Zhang, Y., Li, X., Spencer, R.G.M., Brookes, J.D., Jeppesen, E., 2019. Variability in dissolved organic matter composition and biolability across gradients of glacial coverage and distance from glacial terminus on the Tibetan Plateau. Environmental Science & Technology 53, 12207-12217.


Globally, alpine glaciers hold a large quantity of dissolved organic matter (DOM) and are headwaters of numerous rivers supporting downstream heterotrophic metabolism. However, it remains unclear how glacial coverage and distance from the glacial terminus affect the fate of DOM. Here, we elucidate DOM variability in glacial-fed streams on the Tibetan Plateau using field sampling and bioincubation experiments and compare our findings with the existing literature. We found that dissolved organic carbon, DOM absorption a(254), DOM aromaticity, and the relative abundance of lignin compounds in glacial-fed streams and rivers all increased with increasing distance from the glacial terminus and with decreasing glacial coverage. We also found that contribution of protein-like components, the relative abundance of aliphatic compounds, and DOM biolability increased with increasing glacial coverage and with decreasing distance from the glacial terminus. The ratio of glacial coverage to the logarithmic transformed distance from the glacial terminus was better than that of actual glacial coverage and distance from the glacial terminus in tracing the variability of glacial-fed stream DOM. Microbes in surface ice can produce biolabile DOM that is exported downstream with meltwater. This glacial-fed stream and river DOM is an important source of the highly bioavailable material fueling downstream heterotrophic activity.

Zhou, Z., Li, X., Chen, L., Li, B., Wang, C., Guo, J., Shi, P., Yang, L., Liu, B., Song, B., 2019. Effects of diesel oil spill on macrobenthic assemblages at the intertidal zone: A mesocosm experiment in situ. Marine Environmental Research 152, 104823.


The oil spill accidents may drastically impact the environment and ecosystem at intertidal zones. The spilled oil will penetrate the sediments and accumulate to cause lethal or sublethal effects on the benthic invertebrates. An M-BACI experiment was manipulated in situ to assess the ecological responses of benthic macrofauna to different degrees of diesel oil spill. Both biotic and abiotic parameters were studied for 126 days, subjected to both “pulse” and “press” oil contaminations. The content of aliphatic hydrocarbons (displayed as ratios of n-C17/Pr and n-C18/Ph) slightly dropped then continuously existed in the sediment during the experiment time. The macrofaunal assemblage structures were dramatically altered in species number, abundance and biomass. In general, it takes longer time for the macrofauna assemblages to recover under high concentration oil spill than that under low concentration. Our results highlight the diversified strategies for survival and recolonization among dominant species, which distinguish themselves between: i) tolerant species, ii) opportunistic species, and iii) equilibrium species.

Zhu, F., Hu, W., Cao, J., Ferrante, G., Pasin, M., Zhou, B., Korb, J.-P., 2019. Probing dynamics and wettability of water and oil in conventional and unconventional sandstone rock cores by field-cycling NMR relaxometry. Energy & Fuels 33, 10583-10592.


Fast-field-cycling (FFC) NMR is a technique that can probe the longitudinal nuclear magnetic relaxation dispersion (NMRD) profiles by varying the magnetic field to a large extent. This allows probing the molecular dynamics of complex fluids in confinement. In this paper, the NMRD profiles of saturating water and oil (dodecane) in conventional and unconventional reservoir sandstone rocks are interpreted with a proposed model. In contrast to conventional transverse relaxation studies, the FFC-NMR technique shows very different dynamics and wettability of these two petroleum fluids at the pore surfaces of reservoir rocks clearly. Though there is still no direct technology for in situ probing of the wettability of formation rocks, the FFC-NMR technique showed a potential prospect in the petroleum industry for probing the wettability of continental depositional or interactive marine and continental depositional sandstones.



Thiols (or mercaptans) in crude oils have been considered to be associated with thermochemical sulfate reduction (TSR). However, the molecular composition and the formation mechanism of thiols in crude oils are not clear. This study provides the molecular composition of thiols in several deep strata condensate oils (condensates) from the Tarim Basin. Selective Michael addition products of thiols were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and comprehensive two-dimensional gas chromatography–MS (GC × GC MS). The carbon numbers and double bond equivalents of the thiols ranged between 4–20 and 0–10, respectively. Abundant diamondoidthiols found in two condensates were from high-temperature reservoirs. Various thiol compounds with multiple heteroatoms (S2, S3, S1O1, S1O2, and S2O1 class species) were detected in two other condensates, and low reservoir temperature made it possible to prevent the depletion of the multiple-heteroatom thiols. The pronounced 34S enrichment in H2S and high abundance of thiadiamondoids indicate that four condensates were originally sourced from Cambrian strata and suffered severe TSR alteration. The pathway of thiol formation was speculated as follows: TSR-generated H2S reacts with petroleum hydrocarbons. Deep Cambrian strata in the Tarim Basin has the potential of being a huge hydrocarbon resource, although the high maturity and TSR alteration may negatively impact the quantity and quality of reserves and lead to a high H2S content. The results presented here provide new insights into the TSR reaction, which may assist deep oil exploration and facilitate evaluation of the extent of TSR alteration.

Zhu, X., Chen, L., Chen, Y., Cao, Q., Liu, X., Li, D., 2019. Differences of methanogenesis between mesophilic and thermophilic in situ biogas-upgrading systems by hydrogen addition. Journal of Industrial Microbiology & Biotechnology 46, 1569-1581.

https://doi.org/10.1007/s10295-019-02219-w

To investigate the differences in microbial community structure between mesophilic and thermophilic in situ biogas-upgrading systems by H2 addition, two reactors (35 °C and 55 °C) were run for four stages according to different H2 addition rates (H2/CO2 of 0:1, 1:1, and 4:1) and mixing mode (intermittent and continuous). 16S rRNA gene-sequencing technology was applied to analyze microbial community structure. The results showed that the temperature is a crucial factor in impacting succession of microbial community structure and the H2 utilization pathway. For mesophilic digestion, most of added H2 was consumed indirectly by the combination of homoacetogens and strict aceticlastic methanogens. In the thermophilic system, most of added H2 may be used for microbial cell growth, and part of H2 was utilized directly by strict hydrogenotrophic methanogens and facultative aceticlastic methanogens. Continuous stirring was harmful to the stabilization of mesophilic system, but not to the thermophilic one.

Zilhão, J., 2019. Tar adhesives, Neandertals, and the tyranny of the discontinuous mind. Proceedings of the National Academy of Sciences 116, 21966-21968.


Were the builders of Stonehenge and the painters of Altamira (Fig. 1) cognitively and behaviorally like present-day humans? Did those prehistoric people have language? In the absence of writing, these never-asked questions cannot be answered with direct evidence. However, we take it for granted that, yes, they were, and they did. We do so because we instinctively know that such works require the capacity for abstract thought, deep foresight, and sophisticated communication. In current scientific discourse, this “complex” cognition is set against the simpler modes that can be observed in other species and are assumed to also have characterized our nonhuman ancestors. Hence the question that lies at the core of much paleoanthropological research: When, how, and why did humans acquire language and so-called “modern” (i.e., like present-day) cognition and behavior? Or, put another way, when did humans become, well, “human”? In PNAS, Niekus et al. (1) speak to these issues based on their analysis of a 50,000-y-old flint flake dredged from the postglacially submerged Rhine-Meuse Valley in the North Sea off Holland. The flake is embedded in birch bark tar and is of Neandertal make. It adds to comparable finds showing that Neandertals used artificial adhesives to haft, or better handle, stone tools across their entire geographic range and since at least 200,000 y ago.

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eaogorg.files.wordpress.com€¦ · Web view2020. 2. 11. · GEOCHEMISTRY ARTICLES – November 2019. Analytical Chemistry. Akinlua, A., Jochmann, M.A., Lorenzo-Parodi, N., Stojanovic,